One thing I like about Dominions 3 is that when you take over another nation, you are not able to produce their units. In many other games where this is not the case, the feel of playing a distinct nation tends to be lost since in the end any player can produce any unit (like in AoW).
Similarly, I believe games should require permanent tradeoff decisions. The most fun is when you have to make a tough branching decision on a path for example that closes down other options. I am recalling some of the mechanics in, was it Disciples or HOMM, where once you decided on certain unit, you couldn't go back.
It might make cities more interesting for example if one specialized on calvary, another on archers, another on economics, etc.
It might be too draconian to do the same on magical research paths, but it might be interesting. Again the problem being that if all paths are available, then eventually everyone ends up with everything researched and the distinction between strategies is lost. Thus in Dominions, the endgame for most players comes down to summoning tartarians, wishing for seraphim, etc.
But the idea of choosing a path that eliminates other options, I think makes a game more interesting.