How do you make a unit that only the player can use (no AI units)? Like in RotE 3 with Commander Thire.

That's EXTREMELY easy.
Each class in default maps has numbers following it. Like, most non-rifleman classes have "1,4" which basically means the minimum amount of AI selecting a class (1) and the maximum amount of AI selecting a class (4).
Take the class you don't want the computers using, and in the place where the numbers go, put "0,0". The class will still be selectable, but the AI will not touch it.

Ok, thanks.