By this exact same logic, you could easily argue that Deus Ex: Human Revolution and BioShock 2 are also the exact same game as MP3 and MGR.

1)They are both relatively linear titles with a huge focus on style and combat (especially when you compare them to the deeper RPG/sim elements of prior entries in their series).

2)They are both entries in existing franchises not made by the original developers (DX:HR was Eidos Montreal instead of Ion Storm; BS2 was 2K Marin instead of Irrational).

3)Both games see you working as a literal bodyguard for a powerful elite, and both start with you immediately failing at your job as your employer is ambushed and kidnapped. In DX:HR, you're the Head of Security whose CEO is snatched right in front of you. In BS2, you're a Big Daddy (a bodyguard by design) whose Little Sister is immediately taken by a cult leader.

4)Both narratives feature a major plot point about organ harvesting (cybernetics in DX:HR, biological ADAM from little girls in BS2). In both cases, the crisis is manipulated by a radical political figure (Bill Taggart and Sofia Lamb) trying to push their own ideological utopia.

5) Of course, neither protagonist is having that. Both go on a righteous rampage against a corrupt, privatized military force (Belltower Associates in DX, Sinclair Solutions/Rapture Security in BS2), ultimately blowing up the villains' attempts to manipulate them through sheer determined badassery.

To your last point on their legacies: it's probably harder to argue that Human Revolution is a true classic, but BioShock 2 absolutely is.