The ME series, as a whole, may be my favorite gaming experience of all time. That said, I wouldn't consider any of them as objectively the best games.
I always love to see Ninja Gaiden get love though, I still play it from time to time, because it's awesome. Also nice to see Panzer Dragoon Saga get love, again, because awesome.
I can tell people right now, Digital Devil Saga is my favorite eastern RPG ever, odds are its cousin, SMT: Nocturne is likely the objectively better game. Mass Effect is my favorite Western RPG ever, I think I'd place Planescape: Torment, and KotOR higher in terms of being better games.
Age plays a factor. 8 years ago I would have said Deus Ex is the end-all, be-all of FPS RPGs. Then I played the S.T.A.L.K.E.R. series, and Human Revolution... Some of the luster wore off the original after the graphical improvements, and quality of life changes.
I should say, The Last of Us, along with Shadow of the Colossus, are probably two of the only games I can look at and say: "I find almost no faults here". They may not do what they do best, but they do everything they set out to do with almost no weaknesses. A game that's good to great everywhere is rare indeed.
That said, there are thousands of games I haven't touched, hidden gems I'm sure I'm missing somewhere.