Probably because the Helghast are much more recognisable and the "good guys" all look like generic space marines without the uber aura of master chief. The in both gears and badass marcus fenix or without the magnificence of Gordon Freeman.
If Sev was in the playable character in the other 2 killzone games (and if they were any good) then we'd probably see everyone have ISA avatars.
It's like how a likeable but derivative character like Nathan Drake (he doesn't have any stand out points visually and his personality isn't original for a action adventure ANYTHING) is what people will have as their avatars on the eve of Uncharted 2's launch because he's the only really recognisable character in that series (except perhaps sully, who's awesome) because everyone else looks so damn generic in that game.
Also, the Helghast character models look way better than the ISA (imo and rehashing the generic space marine thing).







