Omanyte/Omastar:
Pros:
- Great Special Attack and fantastic defense
- Good against Blaine and Giovanni
- Alright movepool that utilizes its special attack (Including Surf and Ice Beam)
Cons:
- Bad speed
- Mediocre Special Defense and Hp
- Obtainable quite late (although the same can be said about Kabuto/Kabutops
- Can't really use its rock stab with base 60 attack
Kabuto/Kabutops:
Pros:
- Great attack and defense
- Better speed than Omastar
- Has quite a decent movepool
Cons:
- Can't really use its water STAB
- Mediocre Special defense and Hp
- Defense isn't as good as Omastar's
- Obtained late (Same could be said about Omastar)
So, overall, I think you should use Omastar. It has Water stab and Ice beam, which is quite helpful. Although it can't use rock Stab, Surf and Ice beam should be more than enough. You should also be using Aerodactyl, which is amazing due to both stabs being usable, great attack and speed, and an amazing movepool.
Hope I helped.