Sounds pretty similar to my experience, Panzer.
Cerberus has always bugged. They were evil scientists with a few guards in the first game, and okay their sidequest was fairly long, but it wasn't all that interesting (and it had some annoying bugs, too). Then there was a book that expanded on them or some shit and game two comes around and now they've got spies and agents, which... okay, I'll buy that, I guess. Now game three comes out and they've got this awesome army and shit.
It's like a group's capabilities are inversely proportionate to their feelings towards you. You're working for the Alliance? They need to call up their best soldier to kill a couple angry training dummies. You work for Cerberus? Now the Alliance is crashing meteors in to relays and taking the Reapers all serious-like. Back to the Alliance? Okay, now Cerberus can have giant mechs and animes and shit.
This didn't really need a spoiler tag.
Though I would have thrown a "'combat rolling' can burn with the Whore of Bablyon in a lake of shit until time itself cease to be" in just for good measure.