Moltres or Entei?

IMO Entei for now. 100% cannot ever be topped, while we've already seen evidence of Niantic bringing old raid bosses back (e.g. Articuno).

If you really like Moltres (which I do, I gave mine enough candy to max it), then you'll have the opportunity to max it eventually. I like it's flying dual-typing better to resist Grass. The current grass raid threats are weak to Psychic types though, and Entei with Flamethrower is better for gym sweeping due to the 2-bar and general bulk.

Stats aside, a max 100% is awesome. And don't by any means transfer the Moltres - You can always get more rare candy eventually, consider the Moltres a "WIP"

IMO, the benefit of Entei would be Fire Fang/Flamethrower for better dodging.

I would choose Moltres he is such a power house. He has enough Stamina to last in any fight and his attack stat is so high you can even throw him with your generalist group such as Dragonite and Tyranitar. Entei attack stat is lower than Flareons and is more of a fire tank than anything.