sort of,no,and no.Why not gungans? Because of hatred of Jar Jar specifically? Because of a broader prequel hatred? Aside from Jar Jar, Gungans are actually pretty badass and unique, with their agility, and aquaticness, and interesting design (stalk eyes and long ears), and unique technologies (their shield tech, underwater cities, weird ball explosives and "primitive" usage of spears and animals). And besides, Jar Jar isn't honestly the absolute worst character ever, himself. He's just a really strange/bad decision in the context of the films. But out of context, he's just a not-terrible comic relief character.
I haven't played base JKA in ages, but I think it's this way just because that's the way it was in base JKA siege. The MB2 gamemode is just an overhaul of base siege.Unrelatedly, but on topic inasmuch as we're rambling about little ideas for the future of MB2: Why on earth are the good guys the red team in MB2? The only real explanation I can think of is that the rebel insignia is usually shown as red, but... it's really the light side vs the dark side, and the light side is definitely more of the "blue" side.