Which one?

I would go for the Moltres. It has a higher attack stat and better fire type dps, while quad resisting grass and bug type moves. The higher IVs is also a plus.

Both. Entei and Moltres are different. Moltres throws in the whole flying thing, but has extra weaknesses as well. Take them up together, using the same resources, and gaining the same effectiveness. Neither will be maxed, but both will be better.

Of course, if there's a critical breakpoint you need to reach, go for that, but don't overweight that against increased survivability and total damage output.