[Prepping for the Endgame]

I don't think a bulky grass type really does much for you - the dragon in slot four covers the same resistances (except to ground, which can better be covered by a flying type).  I feel like some sort of speed support could be good, since everything but greninja is pretty slow.  Possibly Tailwind Gliscor or Gligar would do well in that slot, since it gives you a physical wall without ground-type weakness, which complements your metagross pretty well?  

In slot 5, I feel like dragon dance intimidate gyarados could do well?  Gives you the offensive physical attacker you're looking for, but also acts as a sweeper in matchups where you can get a turn for that, and plays very nicely with metagross (against a physical attacker with e.g. earthquake+stone edge, you can use metagross to bait a ground move, get a free intimidate with gyarados, switch back to metagross to take the rock move, and then back to gyarados for a second intimidate, after which either you get a free set up turn from the opponent switching out, or they don't switch out and you get free setup just from the opponent's attack being too low to remain threatening; it sounds like a niche sequence but lines like it turn out to come up pretty often).  Moxie's also an option; you lose some of the pivoting lines, but are a lot more likely to sweep after just one ddance.

 

On Greninja, surf or scald seem better than hydro pump - after miss chance, hydro pump is equivalent to an 88 base power move (110*.8 hit chance), and the spread damage is probably also relevant.

 

[Want Moon stone before beating Keta, how?]

Assuming the item guide is correct, no moon stones are available at that point in the game.  

 

[[SPOILERS] Prize Money on V13 gone]

That's a known bug; install patch 13.01 (link is on the rejuv dev blog), and it should be fixed.

[Please help me beat Shade...]

42 minutes ago, HotDiggityDog said:

What a Huge Power Diggersby? Is it the one with a star next to it, that makes it shine when it enters battle? Don't know what that is for tbh, if you know please let me know... 

Huge power is an ability that Diggersby can have.  The star just means it's not using the default sprite for the pokemon; it's purely aesthetic.  

1 hour ago, HotDiggityDog said:

I got the Carvanha but the Electric Moves completely wipe it out and it doesn't have Crunch, it has Ice Fang, Poison Fang, Slash, and Destiny Bond.

It gets crunch at 40, IIRC.  Regarding getting wiped out by electric moves, if you have speed boost, a pretty good sequence is to paralyze the gengar with Pachirisu or another electric type, then let pachirisu faint, send in sharpedo, get the kill with crunch, and get the speed boost boost to outspeed subsequent pokemon.

[[Warning: Maths] On natures, IVs and base stats]

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).

[Not sure about something...]

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

[Police officer glitch]

It kind of sounds like you might have already saved him; might be worth continuing and seeing if the story follows the all officers found route.

[Ideas of team members to balance]

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.

[Please help me beat Shade...]

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)

[Stuck In Water Treatment Center; Is there a way to save my save file?]

The SWM modular modpack moves the save game location, so it might be somewhere else if you have that installed (I believe in that case you'd want to go to the reborn app, right click, show package contents, and find game.rxdata somewhere in there, but I'm not sure).  Otherwise, are you sure you're in the Library folder that's a subfolder of Users/[your username]?  There are a couple of other Library folders on mac.  

[Stuck In Water Treatment Center; Is there a way to save my save file?]

Should be in /Users/[Your username]/Library/Application Support/Pokemon Reborn by default, although IIRC some mods move it.

[Pokemon Reborn Nuzlocke - Need Help beating Aya]

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.