Huge spoilers here.
Let me first state that you don't have to join any of the factions in Skyrim to complete the main quest.
The fact that people still claim that you are required to join the thieves guild and College of Winterhold respectively when this is blatantly untrue is both amusing, annoying and frightening.

Starting with the thieves guild, to find Esbern in the Ratways you are sent to talk to Brynjolf in Riften.
The thing about the Elder Scrolls games and most good RPG's are that there are more than one way of doing things and completing goals, quests and objectives.
Here you can take him up on his offer and frame Brand-Shei, which means he ends up in jail.
You can use speech, Persuade or Bribe to get Brynjolf to tell you what you want to know without having to resort to larcency.
This obviously means Brand-Shei doesn't end up in the slammer.
You can fail the plant attempt and still get the info or join the thieves guild, Brynjolf still lets you join.
This also obviously means Brand-Shei doesn't do time in the pokey.

There is a reason for letting you join despite your failiure, the reason is that the thieves guild are desperate, they are so low that one of their members is selling snake oil to make ends meet.
The other option is to ignore standing under and following the nice white arrows, taking initiative instead of being led and go search the Ratway on your own.
Using your deductive capabilities to search and explore.
There is also a reason why you can succeed where everyone else fails that you aren't told.
The guild is hit by a curse of bad luck.
You are Hero and heroes in the Elder scrolls games make their own fate, this means you are outside of fate and luck and thus the curse doesn't affect you.
Many things make sense if you know the ingame lore, pay attention and contemplate events and conversations.

Winterhold College:
There are four ways of entering the College.
The first and most obvious one is to take and pass the test Faralda gives you.
If you are far enough along the main quest you can say you are the Dragonborn and prove it by Shouting.
The speech option works here as well, despite people claiming otherwise.
The speech requirement is 100, easily reached either through plain old grinding and training, an Amulet of Dibella, 70 in speech and the persuasion perk, amulet of articulation or Masque of Clavicus Vile.
There are plenty of options to choose from here.
The fourth and last is infiltration, find the cave that leads to the Midden, go through the Midden, bypassing the gates and Faralda altogether.
No joining required.
No spells required either if you know what to do.

Ranks and advancement:
Many people find the rapid advancement in Skyrim to be hugely incongruent and they complain quite vocally about it.
Those of us who have played Morrowind and Oblivion are used to the Imperial guilds and Dunmer factions.
The Imperial Guilds specifically have many ranks and grades, as do the Dunmer factions.
Many think it is strange and nonsensical that you start out as the new kid and soon end up as the leader.
What many don't consider is that the factions in Skyrim are more casual and less formal than the Imperial guilds.
The mages guild and fighters guild have a highly hierarchical structure more suited to the Imperial, Meric and Breton mindset.
The Companions only have Shield brother/Sister, the Circle and Harbinger "ranks", accurately reflecting the more informal Nord mindset.
Compare and contrast the Imperial Legion and the Stormcloaks.
The Legion has the hierarchical rank structure Auxiliary, Questor, Prefect, Legate, Captain, General.
The Stormcloaks have badass nicknames such as Unblooded, Ice-veins, Bone Breaker and Stormblade.

As for rapid advancement that is a staple of Elder Scrolls games. Some NPC members of a faction takes ages to advance.
You as the main character, do not.
To all those who complain about rapid advancement and pacing whatever that means I would like to remind people that the Morrowind main quest can be done in less than 10 minutes, check speedruns on youtube.
From joining the Imperial Cult in Morrowind to becoming Primate, the highest rank takes just a few seconds if you prepare beforehand.
Doing lay almoner and lay healer quests with the resources at hand as well as meeting the skill and stat requirements means you advance from Layman to Primate in less than a minute.
How is that for pacing problems and rapid advancement?

Advancing to the top rank in Skyrim do make sense if you pay attention, both to the overt things as well as the undercurrents, the subtle hints, the understated and the below the surface, behind the scenes going on.
Prime example and frequently complained about is the Companions.
You go from shield brother/sister, to joining the Circle and then as Kodlak potentially within days of joining.
Now let's examine the why's end thereof, the characters motivations.
The most blatant evidence is reading Kodlaks journal, where he states that he dreamt about you, he knew you from the moment he laid eyes upon you, his prophetic dream showing him what to come, he knew you could redeem him and the Companions but didn't overtly show it.

http://www.uesp.net/wiki/Skyrim:Kodlak%27s_Journal

That is one of the reasons for your rapid advancement, Kodlak doesn't show his thoughts directly, but does so indirectly.
Another reason in specific regarding joining the Circle and becoming a Werewolf is that Aela and Skjor are outnumbered 3-2 on the werewolf issue.
Vilkas, Farkas and Kodlak are pro purification, while Skjor and Aela are pro Beastblood.
Bear in mind Aelas motivation, both outright stated and subtly hinted that she is driven by her bloodlust more than she lets on.
She just wants to hunt and kill, not bothering with who or what, as long as she gains glory from the fighting and blood from the hunt.
She doesn't care who she fights, or the justness of the cause.
She just needs an excuse, if even that.
Putting it blatantly, she and Skjor are using you, if you are pro-werewolf it becomes 3-3.
Their plan didn't work out that way, obviously.
Now this is just pure speculation on my part, I have no evidence whatsoever, just a suspicion.
I suspect that Skjor and Aela deliberately picked the Silver Hand as a target to goad them into attacking Jorrvaskr so that they would kill Kodlak.
She cannot attack him directly, but goading ones enemies into doing your dirty work for you, classic ruse.
Another bonus is that he dies as a werewolf, if you hadn't purified him Skjor and Aela would have been able to hunt and be hunted with Kodlak in the Hunting Grounds.
Cunning and bloodlust could explain her kill-happy behaviour.

As for becoming the new Harbinger, let us examine your deeds.
You found all the fragments of Wuuthrad and is directly the reason it was reforged.
You killed the Glenmoril witches who caused the Companions to become werewolves, wiping that stain on the Companions honour.
You killed several Silver Hand leaders, including the dreaded Skinner.
You fought through Ysgramors tomb and in the end purified and saved Kodlaks soul from Hircines Hunting Ground.
You are outright nominated to be the new Harbinger by the soul of Kodlak.
The main meta reason is that you are the toughest hardest, most badass in the Companions.
Your prowess and accomplishments rivals that of the greatest heroes, obviously people will be impressed and reward you accordingly.
Skyrim has a big the strongest shall lead mentality, used by Ulfric to justify killing High King Torygg for example.

College of Winterhold:
You are directly the reason the Eye of Magnus was uncovered.
You found several lost books, quite important books and saved them from being abused by an evil summoner.
You not only went through and survived a Dwemer city that killed many Synod mages but activated and used a Dwemer device.
You saved the College and Winterhold from the magical anomalies, you had help though.
You went through Labyrinthian and found the Staff of Magnus, the same dungeon which killed a big group of trained College mages, leaving only Savros Aren and two others alive, or at the least animate.
The other survivor of Labyrinthian was the hero of Arena.
If you are a lore geek and know the goals of the Thalmor as well as the Elder scrolls cosmology you realize that you didn't merely save the world from destruction or something cliché like that.
You saved Mundus, Talos And the very concept of humanity. You saved humans from being retconned out of existence.
Lastly you have the explicit support and endorsemant of the Psijic Order for becoming Archmage.
That is similar to but not exactly like Saint Alessia saying: This guy is great, he should be High Priest.
With the Archmage and Master-Wizard dead is it so difficult to fathom the reasons for making you the new Archmage?
You get results and what matters is that things gets done, the means and methods doesn't matter as much in this case.

Another important difference between Morrowind and Skyrim is that Morrowind faction quests largely consists of makework, fetch and escort quests, being bossed around like a servant.
Skyrim gets into the meat and bones, the things that matter, the world shattering events, the plot much quicker and the stakes are higher, much higher.
Especially when you realize that Morrowind and Oblivion didn't have any faction quests of huge cosmic significance, Oblivion Thieves guild being the sole exception.
Screw the physical, get metaphysical. Heh...
Skyrim is overall on a much grander scale in regards to quest importance when compared to Morrowind and Oblivion faction quests.
In Morrowind I spend the lower ranks of the Mages Guild picking mushrooms and flowers so that someone else can win a bet.
Mages Guild quests in Oblivion are good in one regard, the foreshadowing, the Bruma quest is a chekovs gun and chekovs skill, but that doesn't ignore the fact that I am looking for a guy, do a prank because the Bruma leader is too bad at magic to find him herself.
In Morrowind my first task in the Fighters Guild was to kill some rats...
Not really on the grand, epic scale of things, is there?
The Oblivion rat problem quest was however amusing, at least to me, with the twist and parody of the Ratstomp trope as well as the continuity and lampshading.

That is not to say that the quests are worthless or completely uninteresting, I particlarly enjoy Edwinna Elberts and Skink-in-Tree′s-Shade′s quests, but Ranis Athrys quests are enforcer jobs or plain old hit jobs for the most part.
Join the mages guild, recruit or kill non-mages guild mages, collect guild dues.
Appearantly the mages staff is meant to break kneecaps.
I am so feeling the magic here...

As for those who lament the loss of the Morrowind system of advancing ranks I am surprised that no one points out the obvious flaw with it.
The requirements for advancing a faction are threefold: Meeting the stat and skill requirements and doing quests.
The stat requirements are met by nearly every level 1 character. 35 in two stats is easy to accomplish.
The skills reqs are one faction skill at 90 and two at 35.
The obvious flaw is that you only need to meet the skill req, but you don't have to know any spells or use those skills.
Trainers and skill books can work wonders.

My Archmage can have 90 in Conjuration, 35 in Mysticism and Restroration but nowhere does it say I have to USE magic or even know any spells.
My Master of the Fighters Guild can have 90 in long blade and 35 in heavy armor and block but I have never swung a sword or worn even medium armor.
One exception is in the Telvanni where you have to know three spell effects, levitate, recall and fire damage, but I never have to use them, just know them.
Capturing an ash ghoul soul doesn't require you to have the soul trap spell since you recieve two scrolls of Fphyggi's gem feeder.
You can get by with potions and enchanted items for nearly all other quests.
In Skyrim however you have to use several spell effects to advance.
The initiation test if you go that route, using a ward spell in the first lesson, Saarthal obviously, aligning the Oculory in Mzulft, Arniels endeavor, Labyrinthian.
For precisions sake it has to be pointed out that some of these can be bypassed using enchanted items such as staffs or even Shouts in some cases.
You also have to meet the skill requirements for the Master spell quests, which can be done with trainers and skillbooks in some cases and other you have to know, use and train with spells.
Then there is also the fact that you HAVE to use the Master spells quest spell to succeed, Conjuration and Illusion respectiely.

Another major problem with this system that few seems to bring up is competence.
Archmage Trebonius is an extremely powerful and skilled Battlemage, but he is an incompetent scholar and administrator, not spotting the obviously fake Telvanni infiltrator.
His curse on Tarer Braryn is a work of art in it's sublime efficiency, but he was to put it bluntly kicked upstairs.
House Telvanni takes the cake though.
The leaders are undoubtably powerful and skilled at magic, but many of them are outright insane, breaking Dunmer laws like using necromancy and Archmagister Gothren is even more extreme in his arrogance, isolationaist and xenophobic views.
The Fighters Guild has some leaders be Cammona Tong or Daedric worshippers.
House Hlaalu has about half be corrupt, extremely xenophobic, Cammona Tong, making deals with House Dagoth.
Oblivion example in the Mages Guild.
Several of the high ranking mages were Order of the Black Worm infiltrators.
The system doesn't require competence, sanity or loyalty, just a static skill and stat req and quests done.
Contrast Skyrim where you become the leader for proving yourself skilled, decisive, powerful, strong, comptetent and not overtly insane.
You have proved your prowess and capability over and over, again and again.
Who else should be the leader? Who else has proven themselves as you have?

Another improvement is the post faction main quest things to do.
In Morrowind once you have done all the guild/faction quests there is nothing to do, at all.
Oblivion did some improvement in that regard, specifically in the Dark Brotherhood and Fighters Guild, praying to the statue for contracts and deciding what to focus on for the guild and the guild master chest.
The Skyrim system is nowhere near perfect, but it is a huge improvement over previous games in comparison.

To end this long, windy, wordy, ranting post I would like to teach the Humility Mantra, which in this case is not Lum.
"Just because I don't understand something doesn't mean it cannot be understood"
"Just because something doesn't make sense to me doesn't mean it doesn't make sense"
"Just because I feel, believe or think something doesn't make it true, correct or even accurate"
"My perception and interpretation of reality is not necessarily reality"