Modern RTS lacks the key part, "STRATEGY"
#1 - The modern games use the rock paper scissors method (rush, boom, turtle).
#2 - All factions are statistically balanced to be equal, sometimes the unit are statistical equals like in starcraft, 2 terrens = 1 protoss in strength and cost, and you get 2 zerg for the same as 1 terren. Some are balenced such that the entire faction is equal to all others, not necessarily individual units having statistical equivalents( this is most now adays). Some like starcraft 2 constantly alter the stats to achieve "balanced game play" because somehow more people playing and winning as 1 faction over another is a bad thing in their minds.
The whole point to having different factions is that they are different. That way you pick the faction the gameplay of you most prefer, this may not be the most "powerfull" faction. Factions should be true to story, and should be scaled to each other in game in accordance with the story.
The players should make the game not the factions.
Like in Elite Force 2, in the specialist games, there are different classes with different stats, the interceptor has 50 HP and no shields and nearly no firepower but has rapid speed. The sniper has powerful weapons which can vaporize in a sinlge shot but moves normal and has little ammo, the heavy weapons spec can wipe out entire teams and moves slow cause he carry's so much stuff, and is heavily armoured, the medic and engineer were much better at helping your teammates and accomplishing objectives .
You played as the class which best fit your style. You didn't play as a sharpshooter if you like to get up close and personal with your opponents, or the heavy weapons spec if you were impatient.
RTS should be that way, it used to be with classic RTS like AOE2 and SWGBG Saga.
Players should make the game, and you should play as the faction which best fits your style, or which you prefer. If you hate large numbers of inf then don't play as the republic, if you prefer armoured warfare play as teh empire or CIS. If you like a straight war machine of lots of troops early and don't mind having to wait for teir 4 to get any good units then play as trade fed. If you like aircraft and durable troopers play as rebels, or navy and aircraft play as naboo, or navy and inf with self regenerating buildings so you don't have to repair play as gungans. If You prefer fortifications and lots and lots of infantry with a powerful air force and Jedi then play as the republic, if you prefer self regenerating high health troopers and workers, play as wookies. You picked the faction which played the way you prefered. No real balance. The players made the game. Plain. Simple. Strategic.
Factions should be unique, and should be true to the story, and should be created with all the strengths weaknesses advantages and flaws which make them what they are.
If a player doesn't like a faction then they should switch to a different one which plays the way they prefer.
Players make the game, not the factions.