They should either make one big tree, or make three interdependently viable trees. But, I shouldn't bitch, as I haven't played a recent beta to really know what is actually in the game.
I agree completely, and it was my stance with the first game too. 5 was apparently perfect and there was no reason to change it until the game bombed completely. Now 3 is the perfect number, perhaps the next one will have just one? At least spell research is removed, for better or worse. So you could say there are half as many trees in FE I suppose. Having multiple research trees that have no dependencies is such a gimmick, but at least things are getting better with each beta 
Just thinking of the Diplomacy tree from the first game makes me laugh a bit. Also at least we aren't researching resources that causes them to spawn in enemy lands anymore! I can't wait till a good Elemental comes out, even unfinished FE is better than the hyped up junk 4x games that keep coming out lately 