Morally, I wouldn't like to fly for EA. Too totalitarian.
GTVA Terran Command is what it is "Try to fly into Lucifer's fighter bays!" and stuff like that. Too stupid.
GTVA Vasudans would be cool except for that I don't specifically like Vasudan fighters or bombers, Terran ships are way cooler IMO... besides, they would likely be too religious for me to handle well.
Nobody knows what the Shivans' motives are, but they are not shown in particularly good light... I wouldn't want to fly for them either. Gorramn star killers.
Well... I don't know a thing about Ancients, except that little amount what the Ancient cutscenes told us. I actually wouldn't like to fly for them either, but at least I don't have any expectations - to either good or bad, so I picked them.
BTW, why is it always so that Earth Alliance ends up as a totalitarian regime?

Anyway, closest competitor to Ancients is GTVA Terrans... the Command's stupidity is not their own fault, after all.