I have just under 800 lobi.. i have virtually ever C-store ship. is the Temporal better than the chimera? is the recluse better than the atrox?

Which captain is the best suited for each?

Not sure about the carriers, but the Temporal Destroyer seems better than the Chimera when geared correctly. Mine is running the Temporal Warfare Set, Omega Weapons Set, Borg Assimilated set, and Antiproton DHC's + 1 AP turret. I am using a Tactical captain, and I routinely get 1st or 2nd place in fleet actions with 11.8% base critical hit rates.

Hold on to it at the moment, lockboxes are going through a rerun. I'm assuming a new lockbox will be out 2 weeks to a month from now. If nothing cool comes out with the new lockbox I'd go Destroyer on a tac toon and recluse on a dedicated healer toon.

The Recluse is about as good as you can get for a dedicated healer, the Destroyer is okay, but not great, in a DPS role, but will be tankier than a Defiant if you run a lt. cmdr engineer. They do very different things, so you can't really call one 'better' than the other.

how is the recluse other than healer?

I have both - Recluse on KDF Sci and Mobius on FED Sci. They're as different as it's only possible.

Both are good ships but I have more fun with the carrier. I've put a tactical boff in the commander seat and dual cannons in forward weapon slots. Coupled with plasmonic leech console it all makes this baby a beast in STFs

I have flown the temporal and the chimera with the same build and the temporal can't be beat. I am flying the Jem Hadar Escort Carrier now and likely do not have the correct build yet but it doesn't seem as hard hitting as the temporal destroyer.