I would give it this set:
Aerial Ace-Covers fighting and Grass weakness (grass weakness is 4X)
Aqua tail/waterfall-Aqua tail for a bit more power, or waterfall for the chance to flinch and a bit more accuracy. also deals with ground weakness
Rain dance-Powers water move and doubles speed.
iron defense/Brick break/Stealth rock/Stone edge/ swords dance- All of these moves are excellent on Kabutops. Iron defense to make him a powerful physical tank, Brick break to deal with screens, stealth rock to damage foe, stone edge for a powerful STAB, or swords dance to make him a lethal sweeper.
Kabutops is a fatal pokemon in the right situation.