The Arcane University premise was pretty irritating: about half of the Mage Guild questline is gaining access to the Arcane University, at which point the dialogue proceeds on the assumption that you're an absolute beginner who hasn't cast a spell before.
At least at the point I started the College of Winterhold questline, everything fit: the spell I was asked to cast was one I'd just learned, and in the first lecture by Tolfdir, I had the dialogue option to say that I knew a ward spell, but had never cast it and didn't really know how to use it -- and Tolfdir's response fit the situation perfectly. The implication was that we'd proven that we had ability with magic, but now we needed theory and training. Then we walk into Saarthal, and suddenly it gets all, "You are the One", and it feels like I'm not just on a railroad, but that I slept through several stops.
There was very little middle and very little end. There are lots of side quests to do in the College, but they basically consist in approaching different college members and asking if they have any side quests available, and it's a little weird to have students asking the archmage to do FedEx quests. The main quest has several deus ex machinas, and leaves a ridiculous number of loose ends. If we've got a reliable oracle in the basemant, why doesn't anyone ever talk to it? What was the Eye of Magnus? What was Ancano doing with it? Why did I need the Staff of Magnus to deal with it, when it seems as if all we needed to do was to shove Ancano away from it? What are the Psijics doing with the Eye? Why are the Psijics involved, anyway? I just angered the Synod and called their attention to the fact that the College has a extraordinarily powerful magical artifact -- how will the Synod respond? I just killed two members of the Thalmor, one of apparently high status -- surely that will provoke a violent reaction from the Thalmor. Why does it all simply stop there? Why do the Psijics get to declare me archmage? Why don't I get a say in who becomes master wizard?
Isn't that a problem with every quest line in this game, even the longest one the Thieves Guild suffers from that problem. The DB, Companions and mages guild are just ridiculious
Oh how i miss the days when you had to... You know... Be a mage to get some headway in the Mages Guild? i think i used spells twice in all of the CoW questline. Once to get in, once to bring down that shield. *sigh*
As for the collapse of the Mages Guild, i think the rise of the Thalmor was also heavily involved. The fall of Crystal Tower would ahve had a detremental effect on the mages Guild as it would ahve resulted in the deaths of many senior mages, and the increasingly insular polacies of the Thalmor would have prevented magical knowlege from leaving Summerset. At the same time, partly in responce to the growing threat of the Thalmor, the Psijics became increasingly insular again, effectivly cutting off the two primary fonts of magical knowlege.
To compensate for the increasingly sparse resources, i imagine many of the Mages Guild turned to Daedric studies, which as the quote previous indicates was illegal.
The Thalmor, the great war and the fall of White-Gold were all long after the MG started to fall apart, about 175 years after... So they aren't involved in any way. You are probably right that the Synod suffered during the Great War, hard to imagine them not too... However the mages guild was already gone by then.