>>20505205first and foremost: don't worry too hard about exploiting; I've beaten both back in the day when I didn't know the optimal strats; you're fighting stupid robots, coverage is king (moreso in stadium 2)
in both games, prime cup and gym leader castle allow mewtwo
you don't necessarily need gen 2 legends (grinding takes forever in gen 2 even with triple speed), but be sure to glitch yourself a mew
for poke cup in stadium 1, psychic and normal spam destroys everything
pika cup only hard-blocks legendaries so if you can get underleveled evos (remember that you can get over-lv100 pokemon to any level via rare candy; it rolls over after 255) they'll be usable there
stadium 1 little cup is a joke; even if you don't exploit, you can do it as long as you have coverage for everything
stadium 1 mewtwo is 6vs1; explosion and seismic toss spam will kill it
for stadium 2's poke cup, alakazam with elemental punches and machamp (cross chop is the best fighting option in gen 2) for dark/normal stuff
little cup: abra, cubone, elekid; I've also found houndour very useful for that one faggot who spams evasion
challenge cup: check you team, just reset if you don't get good STAB to cover most types; shitmons are acceptable as long as the moves are good; shouldn't take too long, I don't think I've needed more than five resets per cup