R.B

Worth noting that you get the ability to change natures around the midpoint of the game (and early game battles generally don't tend to hinge on the specific stats of a given mon), whereas IVs can never be changed except by breeding or a mod, so even if nature is more impactful than IVs (which you've established pretty convincingly), it still makes sense to ignore it when evaluating a mon (at least if that mon is intended to be kept around long-term).

This might be a dumb question, but where's the scripts folder on mac? I see a scripts.rxdata file in Rejuvenation/contents/Game/Data, but no scripts folder.

If you go to the bottom of the post with the v13 announcement, there's a link to the hotfix there.

Do you have Gatekeeper disabled (allow apps from any source to run)? Someone upthread mentioned that solved a similar problem.

Assuming you're on Windows, that's a known issue. Take a look at the post "v13 and MKXP" from the dev blog a few days ago; it discusses the cause and possible fixes for the bug.

For Flygon, I'd recommend Dragon Dance as the last move; a good setup sweeper tends to be pretty useful, and it doesn't look like you have anything in that niche yet. Might be worth considering Galvantula over Eelektross - sticky web gives you some pretty valuable speed control, and I could see bug type coverage coming in handy since medicham is otherwise going to have trouble against bulky psychic-types. (Galvantula's defensive typing is worse than Eelektross's, but you've got ground/electric immunity on flygon and flying resist on empoleon, so team-wide you don't lose all that much, and empoleon can pick up stealth rock if you're concerned about hazards). If you do keep eelektross, I could see a case for replacing stealth rocks with u-turn or volt switch and going assault vest - your team doesn't look very bulky, so it might be hard to get safe switches, and a slow pivot move help with that. For similar reasons, a screens setter like klefki or alolan-ninetails might be worth considering finding a slot for. Edit: Actually, fourth move on Flygon should probably be rock slide. Flinch chance is really strong in doubles, and rock/ground is good type coverage generically. Might be worth replacing steel wing to be able to have both slide and ddance; since it's non-STAB, steel wing will generally do less damage than earthquake even when hitting super-effectively, so it's only particularly helpful against the type-pairs that resist both dragon and ground, which is niche enough that you can just not use flygon in those situations.

Do the team aqua sidequest in Lapis ward; the second reward is a gifted Carvanha. Sharpedo with speed boost and crunch has very good odds of sweeping (Shade's team is pretty unbulky and Sharpedo hits pretty hard (it'll OHKO rotom, gengar, and banette for sure and will probably ohko the dhelmise, leaving the rest of your team to deal with doublade/mimikyu, one of which Sharpedo can take out with destiny bond). Since it's a gift pokemon, it'll also get increased exp, so grinding it up to 40 should be fairly quick. (You can also join team magma, which I believe gets you a houndour, which will probably also perform well, but given that you've already got a good fire type in Charizard, a water type probably slots better into your team, and destiny bond sharpedo puts in solid work pretty much throughout the game)

Throh's pretty helpful against her; it gets wide guard at 37, which shuts off her sludge waves and makes her toxapex almost totally irrelevant. Other than that, maybe bronzor or sandygast? Steel/Psychic is pretty much ideal vs poison, and sandygast gets earth power at 45, which is IIRC the most powerful available ground type move that isn't penalized by the wasteland field effect.