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.