I can understand your confusion. Why would GLaDOS, who is an incredibly interesting, funny, and somewhat well-fleshed out character, get the most iconic position, and still have a relatively flat, dull, stoic character like MC, be ranked higher than a comparatively more interesting and developed character like the Boss?
I don't really see what they're using as criteria. Really, if FPS and space marines defined the decade, then MC should be first, or at least Snake, or Fenix, or (insert manly soldier-type here). GLaDOS and Portal haven't defined the decade. If that were true, First person puzzlers with witty writing and ingenious desing would be the hottest games on the market; and my video game collection would be much larger...
That being said, MC really is more identifiable than the Boss, and I think your criticism, while valid, may be a little off what the pollsters intended. I agree though, I liked MGS much better than Halo. It was better written and more interesting than running around to point A to point B to do the same thing all over again. I tire of space marines really.