Fixed resolutions have nothing to do with whether they are 2D or 3D. All it has to do with is whether support for multiple resolutions was programmed or not. The reason Fallout, Starcraft, and Grim Fandango are fixed at 640x480 is because they are hard-coded to it, not because they involve 2D graphics.
No... the reason games like Starcraft are 640x480 is because that is the resolution the game was drawn at. Blizzard could no go back and make Starcraft run in higher resolutions if they wanted to... you can't do anything to it other than stretch it (and apply filters).
The only way to have those games run in higher resolution is to actually go back and repackage the game with higher resolution art assets. (which is what was recently done with Dragon's Lair HD).
A game's resolution has everything to do with whether or not it's 2D or 3D. Trust me I know, I'm a game designer. A 3D game can be rendered in any resolution you tell it (though the textures and other 2D assets will only be as high as the source resolution), but a 2D cannot go higher than the resolution of the source art. Like I said, the only thing you can do to a 2D game (or any 2D image) is stretch it apply filters...
Think about the difference between a game like Half-Life 2 and a movie like Toy Story. They are both computer-rendered 3D. Yet if you buy Half-Life 2 and install it you can play it at any resolution you want... if you buy the DVD of Toy Story you can only view it at 720x480... Sure maybe you have a fancy DVD player that will stretch it to 1920x1080 and apply some effects and filtering, but it's not true 1920x1080. The difference between Toy Story and Half-Life 2 is that Toy Story was already rendered somewhere, while Half-Life 2 is rendered on the fly by your computer. If you use Fraps and a take a video of Half-Life 2, you are forever stuck with whatever resolution the video was encoded at. This is basically the same thing with 2D games... Starcraft is never going to be high resolution because the art on the disc is not high resolution...