Rotom only has weakness to Grass. that said, Cloyster and Rotom on the team don't clash at all. If you are considering fire types, top one I think of is Heatran.
I had given it some thought, and Cloyster may serve a better place holder in place of your yanmega. Considering both share a weakness to rock, it would be much better to remove Yanmega for team synergy purposes.
Eevees a slow hatchers from what I remember. Do you have a flame body pokemon in your party? cos that will speed the process up a lot. Anyway I've only just popped back online so I can wait.