When doing the main quest there are two times when you are pretty much made to begin the storyline of a faction.
One when you are trying to locate a certain character and the specified way is to pretty much start the theives guild quest chain (unless you asked around elsewhere) and again when you are locating a specific item and the only way to obtain information on it would be to begin a daedric quest or join the college of winterhold.
Of course i can just progress as far as i need to in these stories to get what i came for but then im always going to have those quests in my log for as long as i play that character unless i complete the entire chain.
I also find it breaks the roleplay of my character as i always play as a paragon type who wouldn't affiliate with thieves and murderers.
Anybody else who plays the main quest line kinda feel this way?

What annoys me more than that is being forced to begin the main quest before we can start the civil war quests.

You know you can just find Esbern yourself, right? As for the college, gaining entry there is about as significant as getting a library card, given there are no explicit responsibilities to the organization story-wise until you attend the class.

The MQ and the CW are supposed to be intertwined. Hence why each quest line mentions the other more than once.

And if you think about it, they have to be intertwined. Two event lines that involve the whole of the province wouldn't realistically be able to avoid the other.

It makes sense.

Technically, you can find Esbern without talking to Brynjolf, and there is a way to sneak into the College of Winterhold.

You can't collect the Stones of Barenziah without joining pretty much all of the guilds, you can't complete the Gauldur Amulet without joining the College... the list goes on. It's okay for this to happen when it makes sense for it to intertwine, but when it doesn't, it's just lazy and bad design.

The Stones of Barenziah are rare and unusual objects, IMO it makes sense for most of them to be in the possession of people whose "space" you wouldn't have access to without a good reason. I'm not so much against the locations as I am annoyed by the fact that by the time you find out what the quest entails you've already picked one up and can't even ID it without joining the TG. I'm lucky I can mod in a way to dispose of unwanted quest items, people not on PC aren't so fortunate.

That said, I've already sold the one gem I picked up and I still have the thing in my journal about getting it appraised... but at least when I do find them, I can use them as sources of income instead of passing them by or being stuck with them forever.

What annoys me more than anything is how biased the game opening is. You start out in imperial captivity, and the guy is a complete jerk and just says 'Lol w/e screw the list kill him/her anyway.'

I immediately sided with the Stormcloaks due to that, and I haven't changed since.

That was just one captain, not the whole Legion. And said captain was killed by Alduin, so it's all good with me. I still side with the Legion, I dislike the Stormcloaks for various reasons.