Apologies for the tardy reply.
One of the main design goals of the build tree was to force players to field units that they otherwise would not. In fact, I consider that to be the single nicest thing about Kingdoms: whenever I play, I find myself fielding units I wouldn't field in a tournament, and needing to think about how to use them.
So, to me at least, allowing players to field whichever units they want is not an improvement.
However, there is no reason why you need to be bound by my design choices. I had always assumed that we would post alternative build trees; since the buildings and their abilities aren't printed on cards, you need only print out a few pages of new abilities to have an entirely new game. Unfortunately, other projects have grabbed my attention, and I haven't continued developing Kingdoms the way I had intended to.
If someone did want to develop an entirely new build tree, there are two approaches that I think would be very interesting:
(1) I was very careful that none of the resources you could acquire would change a game of Battleground once it was set up. That is, there are no abilities that give your units plusses to their stats, or anything like that. This was a very deliberate decision, and I think it was the correct one, for several reasons. However, now that the official build tree has been published and is available, I think it would be fun to explore this design space. So, a build tree with resources that allowed you to create veteran units, or magic weapons, or attach heroes to units, or whatever, would be interesting (albeit very hard to balance).
(2) Assymetrical build trees, in which each faction has their own set of buildings, would be fun and challenging to develop, and probably impossible to balance.