Out to the ranges you're looking at (gonna use 300 yards for the sake of the math), on average the 243 will have an inch or two less bullet drop but will also have only 60-70% the energy of the 6.5 Creedmoor. Not surprisingly, the 6.5 Creedmoor will have a little more recoil but still not .308 levels.
Ammo prices are close enough to be pretty much a wash, and I think in normal times 6.5 Creedmoor was actually cheaper. From what I've seen, it also has a better variety of loads thanks to the fact it is also a popular long range competition cartridge. I recently bought a 243 thanks to a screamin' deal, and I can't really find anything FMJ for cheap practice, only hunting loads. Before the panic, I saw "cheap" 6.5 Creedmoor FMJ pretty regularly.
The main thing that .243 has going for it, IMO, is it is a long established cartridge so its not going anywhere any time soon. The 6.5 Creedmoor is a relative newcomer, and while I'm fairly certain it's here to stay if you are paranoid about fad cartridges I suppose that could concern you.
Personally, if I were looking at 2 rifles and the price was close I'd prefer the 6.5 Creedmoor. In your case, I'm not sure I'd buy a 6.5 Creedmoor to replace the .243 for what you're wanting to do; there's just not enough gain for ME to justify it. That being said, I'm also always looking for a reason to buy another firearm so maybe I would.