Meanwhile, I can confirm that training in one school slows down training in all schools. In fact, if you have a University cranking out students, each graduate slows down training in mere colleges and schoolhouses so that the University may create it's next graduate before the minor schools can. You may never get a graduate anywhere other than the University. This system is broken.
Specialists you can't buy from Europe:
1) Expert Tobacco Planter
2) Expert Cotton Planter
3) Expert Sugar Planter
4) Expert Fur Trapper
The only tile workers you can get from Europe are:
1) Expert Fisherman
2) Expert Farmer
3) Expert Ore Miner
4) Expert Silver Miner
5) Expert Lumberjack
As for the educational system, Colonization is on a set timetable. There are only so many experts you can graduate by the time you need to start looking at victory, and at that point you're taking out all your students to make them soldiers.
Making more universities will get you those experts sooner, and with 2 I usually have all the experts I'm going to get by about 1620. After then, it's 50ish turns to graduate and it's just a huge drag on the economy to have 6x citizens doing nothing.
On the other hand, even with 2 Universities you're never really going to be able to make many more specialists than would someone who just had a schoolhouse in each city, for example with John Harvard. The only thing Universities do is speed up your specialist production so you get them sooner, not so you get many more throughout the course of the game.
So, you just need to decide how late you're willing to put off getting your allotted experts, and build accordingly.
As a strong alternative you can ship spare colonists to Indian villages across the continent. Each village has its own diminishing returns on how fast it puts out Graduates, so one doesn't affect the other. You can get about four per village before it stops being worth it, in my opinion. In addition to the four tile workers that you can't get in Europe, Indians also train Fisherman, Ore Miners, Farmers and my personal favorite - Master Fur Traders. Just scout the map out and don't be afraid to travel a while with a caravel to get your Colonists there.