It depends on your strategy. Here is the comparison I always make in such choices.*
Kabutops (more on Attack and Speed, can learn 40 moves of 6 types (it have a lot of absorbing moves, like Leech Life (by lvl up) and Mega Drain (by TM)), and have a 16 physical moves,
HP 60
Attack 115
Defense 105
Sp. Atk 65
Sp. Def 70
Speed 80
Total 495
Omastar (more Def and Sp. Attack, can learn 33 moves of 8 types, but it have 8 Special moves.)
HP 70
Attack 60
Defense 125
Sp. Atk 115
Sp. Def 70
Speed 55
Total 495
*This sentence is by Google translator. Sorry, if something is wrong.