Season 3 is okay. I'd say it's actually the weakest season when viewed as a continuation, but at least viewed standalone it's mostly fine. Though Season 4 helped redeem it in my eyes by retroactively tying the events of GX back into the plot of Season 1 and 2, instead of being entirely an abrupt shift in conflict.
I dunno, I thought the objective of the antagonists in season 2 was pretty weak, no better than 3, but 3 just interests me more, I don't know why. Probably the hottie homunculi, but I'm not sure.