Captain's Super uber mod: More Power, More/Different Viability, More Weirdness. This mod will be built off Joimmons but this is not a slight Joimmons tweak.

Type-chart changes (based on standard type chart not joimmons):
SE:
Poison is SE to normal.
Poison is SE to fighting.

Neutral:
Fighting is neutral to normal.

Resist:
Ice resists dragon.

Critical hits no longer ignore boosts/drops and boosts damage to 140%.
Crit rates are as follows:
normal move: 0%
1 critrate: 1/3 chance
2 criterate or higher: always crit
Additionally, the damage formula *always rolls minimum damage*

Choice Specs/Choice Band: 1.5x both attacking stats.
Black Sludge now heals twice as much.
Accuracy boosts work the same way other stat boosts do.

Old Moves: (all Implemented)

(Poison)
Poison Jab: Power raised to 100. Targets all other pokemon in Doubles.
Gunk Shot: Power raised to 150.
Sludge Wave: 40 power, +1 priority, raises speed 2 stages.

(Ice)
30% secondary chance of sleep (not freeze) (Implemented)

(Ground)
Earthquake: 80 power.

(Bug)
Leech Life: 50 power, restores 125% of damage dealt. Does not work with Big Root.

(Dragon)
Roar of Time:
Effect change:
+2 defenses. (Implemented)

(Seismic-toss like moves)
Dragon Rage: Deals 170 damage not 40. Ground Type.
Night Shade: Power: 60 (Physical). Deals 150 additional damage not 100.
Seismic Toss: Power 40 (Special) Deals 150 additional damage not 100.

(Snore (will likely be nerfed due to lol OP flinch chance))
Snore: 120 power. 90% chance to flinch target. Still only works if user is sleeping. Will likely nerf this.

(Fight)
Rock Smash: 80 power, always lowers defense.

(Priority and Misc)
Aqua Jet: 80 power, raises speed by +1.
Flame Charge: raises attack not speed.
Charge Beam: 35 power, 70 accuracy, raises special attack and speed (50% chance). +1 priority

Weather:
A lot of these mods are aesthetically silly (you'll see plenty of that) but I consider them positive changes to the metagame.
Manually summoning weather through the appropriate move lets it last 12 turns, 18 with Rock.

Air Lock: instead of merely ignoring weather, it changes the weather to "none" completely erasing it until it is reintroduced.
Sand:
now boosts the defense of steel types.
now boosts power (x1.3) of steel moves.
now boosts the speed (x1.25) of ground types.
Sand Rush boosts speed by x1.5 not 2.
Hail:
now boosts the defense of ice types.
now boosts the attack (x1.25) of poison types and boosts poison type moves.
now cuts power of fighting moves to 75%.
Sun:
now boosts the defense of fire types.
now boosts the special defense of poison types.
now cuts power of flying moves in half.
now cuts power of ground moves in half.
Chlorophyll boosts speed by x1.5 not 2.
Rain:
Swift Swim boosts speed by x1.5 not 2.

Abilities:
Magnet Pull: now traps ground, rock, fighting, fire, and steel.
Solid Rock: take half damage from supereffective attacks.

Pokemon mods:
Pokemon mods archive was created by copypasting from Captain's files and Mewtwoforprez's files.
old: is a reference for me, ignore it.
Ability: the abilities this pokemon has.
Moves: moves added to the pokemon's movepool. a negative sign indicates taking it away from its movepool.

Giratina
Ability: Multiscale, Poison Heal;
Status: Implemented.

Forretress
Moves: Recover
status: Implemented;

Ferrothorn
Moves: Rapid Spin, Nasty Plot, Power Gem;
old: 74/94/131/54/116/20
stats: 74/131/113/110/98/20

Wobbuffet
Moves: Taunt, Recover, Magic Coat
status: implemented

Kyurem Black
stats: 145/150/100/120/90/95
Ability: Intimidate/Mold Breaker;
Moves: Ice Shard, Icicle Crash, Earthquake;
Status: Implemented;

Palkia:
Type: Dragon/Water;
Ability: Prankster;
moves: recover, heal order, Heartswap, leech seed, hydro cannon.
Status: Implemented;

shedinja:
old: 16/105/60/45/45/55
stats: 101/80/135/80/110/90
Ability: Magic Guard, Solid Rock;
Moves: Shell Smash, Recycle, Pain Split, Recover;

Rayquaza:
old: 105/150/90/150/90/95
stats: 100/135/50/135/165/115
BST:
Type: Dragon/Dark;
Ability: Air Lock, Thick Fat, Vital Spirit;
Moves: Quiver Dance, Explosion, Spikes, Leech Seed, Toxic Spikes;
Status: Implemented;
niche: I have no idea wtf happened.

Crygonal:
old: 70/50/30/90/135/105
new: 100/50/30/115/240/135
BST: 670
ability: dry skin;
Status: Implemented

Gurdurr:
old: 85/105/85/40/50/40
stats: 85/85/180/70/130/115
Ability: -Guts, Marvel Scale, Sheer Force, Download;
Moves: Blizzard, Dark Pulse;
Type: Ice/Fight;
Status: Implemented

Conkeldurr:
old: 105/140/85/55/65/45
stats: 130/155/115/95/95/45
Ability: Simple;
Moves: Draco Meteor, Dragon Pulse;
Type: Dragon/Fight;
Status: Implemented

Smeargle:
old: 65/10/40/10/40/85
stats: 310/85/85/85/85/85
Type: Normal/Grass;
abilties: Prankster, Magic Bounce, Own Temp, Trace, Magnet Pull;
Status: Implemented;
niche: Smeargle is secretely this mod's haxmon. All obey the haxmon.

Deoxys:
stats: 90/130/90/130/90/150
ability: Sturdy, Mold Breaker;
niche: hey Deoxys isn't just a shitty Deoxys-F and actually has a really nice stat spread.
Status: Implemented

Deoxys-S:
old: 50/95/90/95/90/180
stats: 50/110/90/110/90/150
ability: Moody, Prankster, Magic Bounce, Speed Boost;
Type: Psychic/Fight;
Status: Implemented;

Deoxys-D:
stats: 50/135/185/85/160/110
Type: Psychic/Ghost
Ability: Magic Bounce;
Status: Implemented;

Muk
Stats: 150/70/80/80/90/30
Stench Buff
Moves: Toxic Spikes -Imprison
Status: Implemented: stat buff and toxic spikes added.

Chandelure
Shadow Tag is now legal
Moves: -Imprison
Status: Implemented: Shadow Tag legal, Flame Body isn't.

Azumarill
Stats: 95/55/80/50/80/50
Moves: Belly Drum Ice Shard Mach Punch
Status: Implemented.

Mew
Ability: Adaptability
Moves: Psystrike, Blast Burn, Frenzy Plant, Hydro Cannon Lunar Dance
status: implemented

Manaphy
Heart Swap Buff
Moves: Baton Pass
status: Implemented:  movepool uptodate.

Celebi
Natural Cure Buff
Moves: Roar of Time Frenzy Plant Ingrain
Status: Implemented: Ability unchanged.

Kecleon
Color Change Buff
Stats: 100/60/100/90/120/70
Status: Implemented: stats changed.

Articuno
Ability: Ice Body
Status: Implemented, but Ice Body is unmodded.

Persian
Assist Buff
Abilities: Prankster
Moves: Encore, -Spite
Status: Implemented: encore added, ability changed.

Ambipom
Abilities: Pickup/Run Away
Spite Buff
Moves: Extremespeed
Status: Implemented: movepool update.

Tynamo:
old: 35/55/40/45/40/60
stats: 106/111/126/101/126/111
Moves: Energy Ball, Leaf Storm, Giga Drain, Knock Off, Leech Horn, Outrage;
Status: Implemented;
niche: Tynamo is a bulky pokemon with no weaknesses. it serves no other purpose other than that novelty.