I second Goof Troop. I played the hell out of that game as a kid.
If he can play menu based games, you can play Secret of Mana coop, though you need to progress a bit before you get the girl as a playable character.
The Donkey Kong Country games are pretty good for coop and you can hot swap between players, the GF and I we playing DKC the other day. She'd never played it before and was having a blast even when she wasn't up.
I also lack a lot of 2 player games tho, the snes era was when I became the only gamer in the house and started leaning toward rpgs and single player games more.
EDIT: Secret of Mana isn't really menu based combat, it's more action RPG. But there is the menu system for getting items, and such.