eatch troop is the say for the most part but some come with different trees and some are a little stronger then others...but it boils down to who you side with.

Each faction has a couple of Elite troops, so you'd need at least three different factions to have all the Elite troops at the top of their respective troop trees (Not that you'd know which have which without a chart). You certainly don't need them all as long as the troops you've got work with your play style.

as long as you don't plan to rebel against that faction, no, there is no reason not to fight with only one faction troops