So they both have armor, they both move like cheetas, and they will kick the living crap out of you. But just these similarities make people compare while they are different series. I'm no Metroid or Halo fanboy (even if I do prefer Metroid) but it gets annoying when people attempt to show that one is better than the other.
The thing with both series is that there is some element of mystery, something that we don't know about each character. We don't know who Master Chief is and we don't know how Samus got to be like she is(at leastI don't know). But if you do compare the series, mention how Metroid has made the risky leap from 2D to 3D and still remains amazing. Also how Halo is a multiplayer masterpiece. While doing so, people should stop mentioning the two together because Metroid has no multiplayer (except in hunters) and Halo has never been2D (unless you believe Marathon is part of Halo and 2D series).
I prefer Metroid because it was the greatest NES, SNES, and Gamecube game while halo was (to me) was only "another shooter" and it laked pure variety. Flame me all you want, I'll say all I want.