Regarding faction balance is a tricky thing....
Factions are played different by AIs and humans and if they are good or bad also often depends on the map and so on...
I think In general they are quite good balanced, also you sometimes think they are not, but try another setup/map and you will see.
Not many people play megaglest good enough yet to judge the faction balance ( I think less than 10 people ) . Evry faction has its own style how it should be played. Some are more offensive, others are defensive and so on.
In general I think its not too important to really have 100% equal factionns and sometimes its good if you can adjust a bit in the game setup to get a challenging game for all palyers.