Mass Effect 3: The Deathly Hallows
The Mass Effect story is a three part arc, and even though there are many planet sized fire fights the main show is running into old and very old friends to say your goodbyes. And as my title suggests you can't usher in galactic salvation without cracking a few eggs.
As the final act of Shepard's story Bioware keeps new faces to a minimum. New characters like Vega aren't necessarily bad so much as they're the new kids with nothing to say. And honestly, it's hard to compete with veteran characters like Garrus and Liara, which players have had 30-40 hours to become heavily invested in.
At the end of Mass Effect 2, assuming you didn't make every possible wrong choice, there were roughly 15 squad members total from both games that could potentially fill out the roster for Mass Effect 3. With such a deep well it was a little disappointing to end up with a squad 1/3 that size with no returns from any ME2 characters. Granted, many headlined their own story mission it still felt a bit light.
As far as some of the things people are crying fowl over, like Jessica Chobot and the tacked on COD multiplayer I found them both such small side-shows to the main attraction they never bothered me. To start, Chobot plays such a small part it's a stretch to call her a secondary or even tertiary character. The separate multiplayer mode is fine, but I've never thought of the shooter component of the series as the best part. It's good enough, but for those interested the character progression, weapon modification, and skill trees should keep you busy.
With each passing mission I grew uncomfortable; not for humanity's sake but for that final goodbye. A good story leaves you wanting more, and in almost every encounter I wanted those missions to last just a little bit longer (particularly Thane's). Games may not have the best reputation when it comes to narrative, but when it's done right games can trump any other medium. Mass Effect has done it right.