Advance Wars 2 (most characters), Tawna Bandicoot, Doomguy, Cortana, Zelda, Raiden (Metal Gear), Albert Wesker, various Sonic the Hedgehog characters (most notably Amy Rose), Deathwing, etc.Changing the design of a popular character is very dangerous, and I don't think i've ever seen it pulled off well.
There's a plenthora of characters who've been redesigned and come out better for it.
That said, I'm not arguing that Samus should be redesigned. I mean, technically, she already has been - the Samus that was seen on the NES isn't of the same appearance that she is now, and for better or worse, the out-of-armour Samus we see now has become definitive.