So, that being said, I'm going to have to go with the Collectors as the best antagonist(s) of the three games.
Of course, when we get to the third game, the only way you ever see the Collectors again is in multiplayer, both as antagonists and as a character choice**. As an enemy, the Collectors are by far the most difficult, even in the easier bronze level matches. It could just be my lack of skill, but I haven't been able to win a solo match against the Collectors, even when using my best characters. In the beginning, I dreaded fighting them, since I always seemed to use up my medi-gel and ops packets within the first few rounds, but after a while, I really started to enjoy the challenge (Cerberus gets a little too easy once you play against them several times). Plus, now that I have the hang of them, I really want that Collector enemy achievement badge-y thing that I can proudly display on the main multiplayer menu as I'm waiting for my team to get ready for the next mission. It sounds silly, yes, but I am stupidly competitive, and when I set my mind to something, you'd better believe I'm going to fucking get it. Your days are NUMBERED, Collectors.
* This, I think, is one of the weaker points of Mass Effect 2. There's a real threat, obviously, but what that threat is - beyond colonists going missing - isn't ever really explained. What were the Reapers trying to do? If what EDI said was true in ME2, the entire fleet of Reapers should have different appearances, based on what cycle they came from, but in ME3, we never see anything but the Leviathan-shaped Reapers. And they don't create giant sentient ships with asari, batarian, turian, krogan, etc. bodies; they just become husk-like things with varying levels of toughness and abilities. Harbinger says, "We will find another way" to the Collector dude, but what did he mean by that? Another way to what? Because it doesn't seem like their plans to invade the galaxy were altered in any way from previous cycles? Gah, I'm thinking too much about this.
** I still have yet to unlock the Awakened Collector, but by God, that doesn't keep me from buying as many Premium Spectre and Reserves Packs as I can. His powers are so freaking cool.
Darcblade's Awakened Collector Adept Guide