Yeah I agree about the writing, it seems very rushed. It seems to me like they skipped story to just get you to the action, which is something that just wouldn't work in the Thieves guild, which is why people like it so much.
Just in about 15 seconds I've thought of something that would work better for the companions:
Spoiler Rather than be asked to join the circle and be given the werewolf blood, you could get it by accident. The first time you discover the companions are werewolves, it was an accident by necessity(he had to to stay alive), so why not the same thing later?
Because you already know about the beast blood, you're already partially inside the Circle, you could change the one quest about wiping out the silver hand to one about rescuing the guy that went in there alone; you could be seperated, and while in a room filled with dead werewolves, you get cut by the skinner, which would then lead you to becoming one. Then you could have to go get the totems to become aknowledged by the circle(rather than just to randomly acquire more power), and eventually be allowed to join it at the very end.
The college of winterhold, for example, should have included more mundane quests. I mean, the very first quest is going to explore an ancient ruin? I mean, even that I could deal with, but then right away the main plot device is back at the college, no effort required. It makes you lose immersion, it feels more like Halo where you're just playing out scenes where it skips the boring parts in the middle, where in an RPG those middle bits could/should be an integral part of it. You could have a quest where you have to clear out a secondary sub-dungeon of draugr while casting spells on runes, eventually leading to a climactic scene where the Plot Device teleports to the College.
The trouble with the rebellion plot, I think, is that it doesn't really feel like it's happening. Oh, sure, there are cities with people saying "I hate the Imperials!" Or "I hate the Stormcloaks!", but do you actually see anything happening, outside of quests? So I raid ONE fort and suddenly we own a whole hold? Plus, the soldiers are so evenly matched, I don't even feel necessary. On one of the fort taking quests, i just sat back and watched for a few minutes, and there was no actual chance of failure. Things like that would have been an amazing place for spells like Call to Arms, but they end up being totally unnecessary. Also, you can be wandering in the wilderness and you NEVER see random encounters of stormcloaks fighting imperials. There should be skirmishes happening all over the place, but NOPE, chuck testa.
The Main Quest suffers from the same thing; you slay a dragon, the first one killed in a thousand years, and there is no impact in the main towns. That's a major thing, that's "Hero of Kvatch" level stuff right there, but you get no acknowledgement at all. Another thing that bugs me is that the dragons leave no impact on the environment. If someone dies, their house just sits there, un-owned, forever.
The dragon can go into riverwood and breathe fire on the thatched roof cottages all day long, and nothing is going to happen to them. Sure, It might be difficult to do, but if you have a giant fire-breathing monster, you should at least consider making their breath have an impact on the environment. You could have the actually be able to burn down houses, for example; it would be pretty simple, just make it so the roof becomes all firey, major blaze(kinda like giant camp campfires), and when the player leaves the cell for a few hours it changes the house to a burned wreck.
Then, have a bit of dialogue about "Well, we've lost everything before, but we'll rebuild!" from the owners, along with a building animation with hammers and stuff, and if you wait a few days ingame time you come back and it's back the way it was before. See, not all that hard, and it would really have made for an immersive experience. Heck, you could even make it so the player could put out fires with an ice spell, if you want.
When i look at Skyrim, i see a game chock-full of unfulfilled possibility.