The blankity-blank protaganist works best in games where the main focus of attention is on something else much more interesting. Bioshock, for example, is a game that I can't imagine would be much improved by the addition of a protaganist personality, because it would detract from the focus on Rapture. Plus, I can't imagine any personality that wouldn't respond to the entire experience with something along the lines of "Aaaargh, this is so fucking creepy!"Blanky McEveryman: Savior of Worlds.
This, I think, was the problem at the heart of the Metroid: Other M brouhaha. The problem wasn't that they changed (or ruined, depending on your opinion) Samus' personality but rather that they added one where there really hadn't been one before and changed the focus from the enivronment to the protaganist. Of course, it didn't help that a lot of people didn't actually like the new personality, but that's a whole 'nother discussion and one I'm really not interested in getting into.
I certainly don't disagree with you though, there are definetly games that would have greatly benefited by giving the player character something to do other than just defeat all the challenges that appear in front of them.