So yeah, this is essentially a place where the community can work together to generate ideas for mechanics and stories which can be used by themselves or others to expand the existing guild questlines to something more befitting the Elder Scrolls name. Many of us aren't yet experienced enough with the mechanics of modding to do anything useful in the various mod teams which are popping up, and will pop up, but we can at least freely give our ideas in the hope that they prove worthwhile until our skills develop.
The various guild questlines in Skyrim are...well, underwhelming. They all appear to have a similar set of problems; too few missions, poor pacing, and a lack of any sense of character advancement. In Morrowind there were skill requirements to advance in the guilds, in Oblivion you had to travel the world doing work for each outpost of the guild before being trusted with the big stuff, but in Skyrim, you're given a quest to induct you, a quest relating to the guild's lore, and then 2-4 quests which cover a storyline culminating in you becoming the guild leader.
The first issue as I see it(having completed Mage, Thief, and part of the Companions), is how to tie additional content into what already exists without completely abandoning it all. Is it feasible to insert new material between the existing quests, or is it better to just "intercept" the player before they begin the existing content, and direct them into a fresh stream of quests which culminate in them doing the existing content? Do you prefer the idea of front-loading the content in that fashion, with an accompanying increase in the difficulty of actually joining and leading each faction, or do you prefer the idea of leaving the existing quests intact and just adding new content on at the end revolving around guild leadership? Do you have ideas on how to combine both methods?
At least in the beginning, the Thieves have an advantage in this regard, because of the gem. Currently, the "mysterious gem" just leads you right to the guild itself in Riften, and launches you into the main quest, but it should be fairly simple mechanically, to my understanding, to change that so that the gem directs you to the mod content first, either by just changing the location to wherever and having the "appraiser" be a new questgiver, or if you wanted more of a challenge, by having the "appraiser" be an actual jewel appraiser, who upon inspecting the gem, finds an inscription -either directions or a riddle of some kind- which can lead the player into the custom content. For players who just stumble into Riften as part of their wanderings, the issue becomes the same as with the Companions and the Mages - the NPCs which "invite" you into the respective guilds are already fully voice acted, and so adding new options would require them to be completely reworked.
In terms of inserting content prior to allowing the player to access existing storylines, the Companions seem like the simplest fix, as they already have a mechanic built into their story which requires the player do do some questing for members before getting to the meat of things, the only issue with that mechanic is that it only requires you to do one mission. Altering the conditions for triggering the more advanced sections of the storyline to force the player to do a couple of Radiant quests for each Companion, and perhaps even achieve a certain level in one of the "warrior" skills, will from my understanding be a simpler undertaking than setting up such a system from scratch for the other guilds, and integrating it seamlessly into the existing world.
The Mages would appear to have ideal questgivers in the form of the Court Wizards, but I'm not sure how one would go about adding new content to them, and not using them in some way feels like a bit of a copout.
Anyway, all thoughts are welcome, have at it.

I will try and think of some more and some more detail but for now there's something for people to think about.