I still think you are on the right track with the .22-250 choice. Lot's of factory ammo. Minimal recoil. Great power (for prairie dogs.) Heck, everything is going to get pushed around by the wind, so won't matter much between a .243 and .22-250 as your Dad is going to have to learn to 'kentucky windage' his shots either way.
But if you are seriously thinking he MIGHT want to shoot Bambi someday, the .243 Win makes more sense. Just know that a long day on the prairie dogs with a .243 Win will be more punishing (recoil-wise) than the .22-250 would be. As we get older, we like recoil less and less. Since the primary goal was prairie dogs, go with your first instinct (it was a good one.)
I was going to suggest the .224 Valkyrie as an option since it will be twisted to shoot heavier for caliber bullets, but I'm not sure it is going to survive long term. Still...it's an option if you are looking to 'fight the wind' without the recoil of a .243/6mm gun.
EDITED ADDITION: Re-read the original post and...since this is for your Dad and HE expressed an interest in the .22-250 Rem, that's what you should get him. He'll be happy. It's what he 'knows' and that means a lot.