Prelude:

They are constantly changing endless, with trainer changes coming soon, and with the biome changes that were released, it nerfed setup mons quite a bit, they're still strong, but losing buffs every 1-5 floors is difficult for that strategy to carry throughout everything.

Biome changes – 20% / 40% / 60% / 80% / 100%, the chance goes up per floor clear.

Starters:

Try and start with as many shinies as possible, with 15 cost you it is ideal to start with a strong mon, or a mon that can fuse to become something strong (fusing is amazing mid-late game) bringing Pokerus if possible. Having a legendary carry you is great, but difficult to get started.

Fusing Shinies allows the luck stat to add onto itself, allowing you to have more helpful team members later on, and allowing you to stack your luck stat higher and higher,

Recommending bringing mons with strong egg moves, recommendation of farming out a good passive. Recommending tinkaton / mawile as starters would be great for 250, ideally having either huge power passive on Tinka, or Swords Dance on Mawile / Tinkaton.

Early game: 0-1000:

A very early breaking point is 50, if a run dies @ 50, don't feel bad, that's the hardest part of early game. Recommend bringing Pokémon with Steel, Fairy, Ground moves, as most paradox mons have a weakness to these moves, with the exception of Iron Leaves, and Iron Bundle. Both of which may require a second Pokemon, but ideally you kill waves 50, 100, 150, and so on in one hit before they can gain stat buffs, and become very threatening. (No longer able to setup before hard waves)

Emphasize how strong Candy Jar is, recommend getting as many as you can as early as you can. Exp Balance isn't the Worst item, but avoid picking it up if you can. Using 1-2 strong mons for early game is ideal. Berry Bag / Lock Capsule should also be 100% pickups, as they both are a great permanent buff to your team.

Running a mon with pay day, or make it rain for early game income is also a great choice, as later in runs you’ll have better self-healing options / money from nuggets + amulet coins. Saving a good chunk of money for healing up carries before bosses is a good strategy, in case they’ve taken heavy hits or need elixirs etc. Having a pickup mon early game also helps with item acquisition.

If your party has the capability to take on double battles, recommend lures for more xp.

Eternatus on 1000 will have Black Hole, amongst a ton of items, ideally you'll have a fairy/steel fusion or tinkaton / mawile. Try and move all your leftovers onto another mon if you can. Using them with as few healing items as you can to shorten the amount of time you spend in the fight to keep Eternatus battles short, to reduce the amount of items Eternatus will steal.

Mid-Game 1001-2500:

Starting on floor 1001, Pokemon will have 5 recovery tokens, healing 15% per turn, every turn. Still viable to be one-shotting most mons by this point, and hopefully you have 30-40 candy jars, the more the better.

Stacking vitamins on your carry Pokemon (Protein / Carbos / Calcium) will allow your mon to gain up to a 310% stat increase in that stat, stacking with Soul Dews, you can gain great amounts of damage increases which become more helpful the higher up you become. Your mons IVs determine how many vitamins your mons can take, so trying to find mons with a high Atk/SpA stat allow for great increases in damage. This can be started earlier than floor 1k, but should hopefully be at least 1/3rd of the way maxed by this point.

Hopefully by this point you've caught a Garganacl with Salt Cure, or have the ability to start progressively increasing the amount of money you have. Rerolling at this stage should mostly be used for Shiny Charms, if that's what you're looking for, master balls for catching dangerous bosses, and DNA splicers to solidify your team.

Ideally within these 1500 floors, you'll find a Metal Burst Pokemon, a Pokemon with Sturdy, and a high base HP pokemon, or a mon with high HP IVS, to stack HP Ups on, as the more HP you have, the more damage you'll be able to do late game.

Try and catch a shiny mon with run away, or just a pokemon in general that has the ability Run Away, as it becomes very helpful post 2k, mainly used in 2500+.

After Floor 2000, mons will get another 5 recovery tokens, healing for 30% of their max HP per turn, and when paired with berries, the most mons will usually heal for is 55-80% of their HP per turn.

Late Game 2501-5850:

Congrats! The end is near, be ready for a lot of running away, or long battles.

By this point, you should hopefully have a mon that has Sturdy, Metal Burst, Leech Seed, Protect, and Salt Cure all in one. (Leech Seed can go on another mon, if you've got prankster on it.)

Soak is also a very nice move to have, as it +salt cure + leech seed counteracts the 30% HP mons will recover every turn, dealing 37% hp per turn, which can be very helpful against mons like Eternatus.

Running away from most fights post 3k is pretty helpful, as normal moves/mons start falling off at this point, with the amount of damage mitigation tokens becoming incredibly high, and dmg increasing tokens also hitting incredibly hard, mons without focus bands / sturdy / endure will not be living more than one hit, while the enemies will almost stop taking damage by this point.

Having a mon with Misty Surge is also super helpful, as it prevents your mons from being status'd by the tokens, allowing you to hit metal burst every time, instead of rolling the 2/5 chance to be Slept / Frozen. Also, Prankster + Soak & Entrainment allows for you to take on mons with Mold Breaker.

Having a fast mon that can flinch is also ideal, as occasionally you may run into double battles against the paradox mons every 50 floors, which can be run ending, and incredibly hard to fight. Trying to make them focus on one side, and resetting to figure out their moves is perfectly understandable. Using F5 or reloads for endless is totally understandable and by this point probably encouraged.

Keep in mind any Pokemon that can have Shadow Tag, Arena Trap, Neutralizing Gas, and Mold Breaker can be difficult to deal with as boss mons, as Shadow Tag / Arena Trap keep you from Running Away, while Neutralizing Gas / Mold Breaker both let them hit through sturdy, scary mons eternatus can fuse with would be Reshiram / Zekrom, as they also get Mold Breaker (Turboblaze / Teravolt) and can hit through sturdy mons. At that point, try and bait Eternabeam with another mon, sacrificing it (if you don't have a fairy type to eat it), or have a mon that's Fairy/Steel with Unnerve, and all of the aforementioned moves, Salt Cure, Soak, Leech Seed, but not Metal Burst, running Ruination / Nature's Madness as you can never hit it back.

And, that's about it! Running away and throwing MBalls at any shinies you see / Shadow Tag / Neutralizing Gas mons is the best use for them. Being underleveled at this point is completely understandable, and perfectly ok, as Soak + Salt Cure + Leech Seed dmg bypasses level, if you're reliant on that. Adversely, if you are relying on Metal Burst dmg, trying to level up and metal burst as many mons down as possible is probably the best way to do it.