I want to start by saying that I really liked the system in Daggerfall where you not only needed to complete quests to move up in a faction, you also needed to express a certain aptitude in the factions main skill group (I think this system was still present in MW, but the skill required was too low for my tastes and was modded higher). Luckily, Skyrim has conveniently given us a set of arbitrary stepping stones with the spell levels. What I see is this: expand the practice sessions for spell casting to include all of the spell schools over several days. Add a repeatable quest to do in between "Good Intentions" and "Revealing the Unseen."

If the player gets a skill to apprentice (shouldn't be too hard, even for non-optimized races) by the time these "learning quests" are done, you are sent to Saarthal with the others. The next quest is also fine at apprentice level, but "Good Intentions" should be held until adept level. A few quests can be added in between, but it might be just as good to have a courier approach you when you hit 50 in a skill telling you to get back to the college if you aren't already there.

Unfortunately, once you get back from the dwemer ruin (Revealing the Unseen), things start to move pretty fast, so it would make sense that you aren't sent out there until expert level. Stopping the story after this quest just doesn't make sense, so the player should be ready to take on the role of arch-mage by this time. Perhaps before getting sent out there, a quest similar to "Aftershock" is set up. This would be repeatable and would send you to a random area to take care of some atronach on the loose or something. The reward wouldn't be gold or items, however. It would be a free training with one person. This way you are guaranteed to work on leveling up your skill to be assigned the task of heading out to Mzulft.

It might be a bit much to require 100 in a skill to become arch-mage, so I'll leave it at starting "Revealing the Unseen" when you are expert. The rest of the quests follow with too much urgency to require any more in between.

I'm pretty sure half of it didn't even make sense. They opened up a whole new plot thread with the Synod in the Dwemer Ruins, but it went absolutely nowhere. The discussion you had with him was building up to something that seemed important, but it may as well not have happened at all. If he hadn't been there, what would have been lost? If the Arch Mage had given you the focusing crystal to add to the machine instead of the Synod mage, nothing would have been affected.

I was really confused with how it all ended. The 'bad guy' was obvious from the start, which is always something you should avoid. If it had worked out differently, perhaps with the Arch Mage being corrupt, and Ancano being there to investigate claims of corruption in secret, then that could have been at least some sort of twist. But no. Evil looking Thalmor is evil. The end.

the Synod

I had hoped the Synod story would go somewhere, like being able to return to Mzulft after the Eye had been taken away, to see what the Synod was actually trying to find out with the machinery. After all, it was the power of the eye and the staff that caused the interference on the map that messed up the Synod's plans. So what were those plans? It sounds like it involved tracking down powerful sources of magic using that map. With the interference from the eye gone the map should have started showing those things, and that could lead to a new series of quests involving the Synod.

I did have some plans involving a large dwemer ruin, and the map and the Synod could fit in there perfectly.

As for the map in Mzulft, I had assumed they were looking for the staff, and when he saw the other big dot at the college, he got all pissed about it. I ended up killing him because I didn't want him to report back, so I'm thinking that if you do want to continue off of that story, you are either going to have to make him essential (bad idea), quickly recall out, or keep the option to kill him, but have a Synod search party come in about 2 weeks after to continue the story for him.

Adding some story to the Psijics would be great too.

I thought the Eye of Magnus bit was very ingenius, and I expected a lot more out of that story.

The Synod guy kept saying that the map should 'lit up like the night sky' which indicates to me that there were supposed to be many more dots on that map (like stars in the sky). If he was after the staff of Magnus he wouldn't be so angry, because it did show the location of the staff on the map.