Makoto: If the Phantom Tribe thing never came up, his powers of manipulating old machines would be utterly useless.
Nanami: If I'm right, her abilities were to have excellent cooking skills? These are worthless because she was already a good-enough cook back on Earth, she sold Lunch-Boxes back at School.
Jinnai: Jinnai doesn't even have to be in the Story, he can communicate with the Bugrom and that's about it, Queen Diva can do that herself and I'm sure she'd have done a far better job at commanding the Bugrom if Jinnai had never come along. Whereas Jinnai does a good job, his lust for power always seems to come in the way which results in his "ATTACK! ATTACK! ATTACK!" thoughts, leading to his defeat.
Probably Makoto's technology interface, for example, based loosely on Alternate World, would suggest he had the same DNA for clearance as an Administrator type on the technology systems, as the advanced civilization used that in favor of just raw passwords and the like.
If you were ended up or transported to El Hazard, what kind of powers you'd like to possess?