This has already been said, but Halo is an FPS, and Starcraft's a RTS. You can't really compare them in terms of gameplay. The comparison might be valid when/if Halo Wars comes out, but that's in the future.
Even so, they do have something in common IMO:
Both are solid games, albeit horrendously overrated in some circles (Total Annihilation FTW) - especially the storylines / single player campaigns in both games.
Both series will have / have already had sequels consisting mainly of a graphical facelift and some minor gameplay tweaks.
And both games have their small share of fans who would qualify as fundamentalist zealots in religious groups.
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