I am so sick of this!!! I'm pretty sure this problem was in Oblivion too, but I'm doing the Mages questline, and the main quest, but I'm doing them simultaneously, not do one till its finished then do the other. This is not a linear game, I can do what I want. Most of the time. Right now, I can't continue the main quest and get knowledge about the Elder Scroll until I beat that badass Dragon Priest. Neither can I turn in the Shalidor's Insights quests because that bloody Staff of Magnus quest is blocking them both. When I talk to that stupid orc moron in the library place all he says is 'Do you think Arcano knew what the eye was really capable of?' Man it is so frustrating. I hate this sort of thing, quests should be able to be done in any order, I shouldn't have to do a mages quest BEFORE I continue the main quest.

It is very satisfying Fus-ro-daring his books and crap all over so he's left with a totally messed up library. He even said 1 thing different: Watch what you're doing, to which I said '[censored] YOU.' lol

I know how you feel. I cannot progress with the companions questline because it clases with a quest the stupid Jarl of Winterhold gave me.

Curious, we did shalidor during magnus...?

It is frustrating but I think once the "problem" with the Eye becomes significant, it's a bit unrealistic to expect the mages at the College to say "oh sure we all may die and the whole world could implode at any minute because of what's going over in our training hall, but let me stop what I'm doing anyway and help you track down some info on a completely unrelated subject." I think we get an almost ridiculous amount of leeway in putting off certain things in various questlines, and given everything that's possible and everything that's going on the game world, IMO the conflicts between intersecting questlines are fairly rare and the ones I've come across do make sense for the NPCs involved.

/\ This +1

wait, theres quests that conflict with eachother?

other than npcs acting like muppets only being able to be aware of 1 thing a time i was not aware of this

With reference to the College of WInterhold, there are NPCs there that you need to talk to in order to progress through both the MQ (altho I suspect this can be skipped if you already know where to go next) and the Thieves Guild quests, and probably some others that I've forgotten or haven't done yet. In particular with the TG, there is a mage that you have to deal with repeatedly for a while.

But if you start the CoW storyline and let it get to the point where the Eye (and Ancano's intentions with regard to it) have become a serious threat, nobody at the College will talk to you about anything else until you deal with Ancano and the Eye, which means finishing out the College's main questline. It then becomes impossible to progress in any other quest that requires help from anyone at the College until you finish the CoW quests.

It's not so much that the quests conflict or bug out, it's that they intersect in ways that will determine when and in which order you must finish them once you start both and reach the intersection.

This. My second character decided to do the Daedric quests early, and so visiting Sigmus' Outpost lets you get the scroll before that part of the quest. By the time I needed it for the main quest, I was tired of seeing it in my inventory. There was a dialog option to tell Parthy that i already had the scroll right after he mentions that it's needed.

I wasn't sure it would work but it did, and it was pretty seamless and skipped a lot of the "back and forth" in the CoW talking to people. It's now my preferred way to complete that part of it.