The specific issue with GURPS and Supers has to do with scaling. If you have enough points, it's fairly easy for a Superman-type to get +100 damage to their attacks, and they can also buy DR 100 against all attacks. They end up punching for 2d6+100, which means they can meaningfully interact (through punching) with anyone who has DR in the 90-112 range; if they go slightly outside that range, then the fight is over in one punch, or it's impossible.
Meanwhile, Batman is out there with his 4d6-damage exploding Batarangs, and he has to really hope that Zod doesn't bother to look in his direction, or else he's dead before he has a chance to react.
GURPS doesn't generate comic book stories. GURPS tells us what would happen if these characters existed in the real world.