There's something I've been thinking about regarding Mass Effect 3, and the Mass Effect trilogy in general. BioWare stated that Mass Effect 3 would more feature a more direct foil to Shepard than the previous games, which seems to have been intended to be Kai Leng. I'd like to look at Shepard's major adversaries in all three games, and see how the adversaries in Mass Effect 3 stack up in context.
Despite the presence of several secondary opponents (Matriarch Benezia, the Thorian, even sometimes the Council), there is no question that Saren was the clear primary antagonist and foil for the hero in the first Mass Effect. He is woven through the main plot of the game, from the first mission through the last, and is both a menace to galactic civilization -- humanity in particular -- and personal enemy of Shepard from almost the very beginning. Besides attacking Eden Prime and plotting the return of the Reapers, he also opposes Shepard specifically by denigrating the Commander in front of the Council, sending assassins, and eventually fighting personally at Virmire and the Citadel. Saren works well as a villain because he's both a danger to everything Shepard is sworn to protect, and a rival who seeks to stop the Commander specifically. This gives encounters with him an added punch -- the player is motivated to fight Saren both to save the galaxy and to defeat a personal nemesis.
Another aspect of Saren that makes him an effective villain is that in many ways he is a darker, more powerful mirror of the hero. He's a Spectre, like Shepard though much more senior and respected, but he is a Spectre who has been corrupted and uses his power to destroy what he's supposed to defend. As the story progresses and more information about the Reapers is revealed, an additional parallel develops -- Saren knows more about the Reapers than Shepard ever does during the course of the first game, yet he chooses to serve them rather than fight them.
The fact that Saren is a well-crafted villain improves Mass Effect by making it more satisfying to oppose him, and the fact that he's like Commander Shepard in important ways makes it more meaningful to either defeat him in the game's penultimate battle, or convince him that he is wrong, leading to his suicide.
Mass Effect 2
In Mass Effect 2, while the Collectors as a whole -- and the Reapers behind them -- are presented as the villains, I would argue that Harbinger specifically is the primary antagonist of the game, and that he makes an effective personal adversary for Shepard. From the middle of the Horizon mission onward, whenever the Collectors appear, there is always a Harbinger-Collector present, and while there is no actual dialogue between Shepard and Harbinger, his personal interest in Shepard is obvious. Both before the events of the majority of the game, where the Collectors attempt to recover Shepard's body to make sure the Commander stays dead, and during the game, where quotes from Harbinger such as "You will know pain, Shepard," or "Preserve Shepard's body if possible," are common, Harbinger's interest in the hero is obvious and at times even disturbing. The contempt Harbinger voices toward Shepard in combat also intensifies the feeling of personal conflict. As with Saren, this makes him a more effective villain, able to motivate the player to stop him both for duty and for personal animosity.
While Harbinger is in no way a mirror for Shepard as Saren was, the extreme difference between him and the Commander improves his effectiveness as a villain in a different way. Harbinger is a being of far greater power than Shepard -- even though the Collector General and the Reaper Harbinger are never fought, his avatar on the battlefield is usually the most powerful being present. The Harbinger-Collector's power is made even greater by Harbinger's ability to make another Collector his avatar soon after his previous avatar is defeated. Shepard is characterized as being like an insect or bacterium by comparison. Rather than a rivalry between similar characters, such as with Saren, the conflict with Harbinger is presented -- at least by Harbinger -- as one of a powerful being dealing with vermin. This makes it more satisfying to fight him, and to foil his plans, in order to prove him wrong. And as in the first Mass Effect, the presence of a well-crafted villain makes Mass Effect 2 more enjoyable to play.
Mass Effect 3
Unlike the first two games, Mass Effect 3 does not have a well-defined individual villain. The Reapers as a whole are the source of the game's conflict, but unlike the Collectors, who had Harbinger to represent them directly, the Reapers of Mass Effect 3 are a faceless menace.
Is there anyone who functions as an antagonist for the game? Kai Leng is seemingly cast in this role, but other than a brief cameo with the Illusive Man near the end of the Mars mission, he does not appear until fairly late in the game -- later than Harbinger, if the player has been doing all the side missions available before the Cerberus attack on the Citadel. While he will mortally wound Thane or outright kill Kirrahe, and proves troublesome for substantial portions of the mission, he has little interaction with the player. He appears three times more after the Citadel -- at Thessia, where he engages in an inconclusive battle with Shepard before stealing the data from the Prothean VI, at Horizon, where he's long gone before Shepard arrives, although depending on the Commander's previous decisions he may have fatally injured Miranda, and finally at Cerberus headquarters, where he engages in a last battle to kill or at least delay Shepard. While Leng certainly seems to see himself as a rival to the hero -- his email after Thessia makes that clear -- unlike the darker, more powerful mirror Saren or the incomprehensibly superior Harbinger, Kai Leng comes across as weaker than Shepard, and envious of the Commander's skill and fame. Rather than a worthy opponent, he falls more naturally into the role of an obstacle, or an annoyance to be brushed aside. Additionally, he suffers from being explicitly the Illusive Man's minion, rather than his own master as Harbinger was, or at least giving the appearance of being his own master as with Saren.
I would argue that, while there is no character in Mass Effect 3 who functions as an antagonist in the same sense as the previous two games, out of all the enemies present, the Illusive Man comes closest to filling the role. He appears early in the game, and while he never fights Shepard directly (at least using the normal combat mechanics of the game), he is frequently at odds with the Commander and the forces at his command cause the player much grief. He shares some of the same parallelism with Shepard as Saren: he at least nominally seeks what's best for humanity, similar to Shepard's goal to save humanity or galactic civilization as a whole, and he is also knowledgeable about the Reapers, much like the Commander. Most notably, he makes a personal appearance to oppose the hero in the final scenes of the game, after Kai Leng has been dealt with, and in a scene that carries much more dramatic weight than the last confrontation with Leng. While he is not responsible for the principal conflict of the story, and his defeat contributes little to the resolution of that conflict, for storytelling purposes the Illusive Man is the closest thing Mass Effect 3 has to a primary villain.
In the end, the first two games of the Mass Effect series benefited from appropriately menacing villains, who gave the player additional motivation to win the games, and made victory more satisfying. Whether the lack of a character who fits well into the role of a primary antagonist reflects weaker writing in Mass Effect 3, or whether it is the result of a deliberate artistic decision, it marks another significant difference between the third game and its predecessors.