Like Lucius I mainly use Hero for fantasy. However I could get behind a more clear delineation between Fantasy Hero and Champions. Ever since 4th ed FH has been Fantasy Champions, all in the name of unified system. Unfortunately, for all its versatility, Champions has issues when ported to fantasy. One, it's not costed correctly--Flight is too cheap, and STR absolutely needs to cost 2/pt if it defines how much damage your character inflicts and what its defenses are. Two, more areas need to be better defined, including but not limited to magic, healing, magic, spells, magic, armor, skills, special effects, and sorcery.
I don't think we need to go as far as actually having two sets of rules for the different genres. I'd be more inclined to have generic Hero underpin all genres and institute a campaign-preferences system that lets GMs tweak things like the CV range, cost of certain powers and stats, access to powers, and so on. Then we would put out slightly more genre-specific versions of Hero, to lower the learning curve and make the system fit better. And once players catch on, if they want to start tweaking the rules, the crunchy stuff is there to support them.
Anyway that would help prevent the genres from holding each other back, if it actually happens.