1. A thin plank with a muddled middle makes a curious cure (SALT) -- Anagram
A thin plank is a SLAT; we can rearrange (muddle) the middle two letters to get SALT, which goes with cure to make Salt Cure. I understand why it's called that, but it's still curious that the "cure" move just hurts you.
2. One of the twins is a bottomless Latin American (LATI) -- Deletion
A Latin American is a Latino (or Latina (or Latinx, although all my LATAM friends hate that word)). Whatever it is, if you drop the bottom letters you get LATI. One of the Lati@s twins is a singular Lati. I really wanted to make something with "Lati@s/Latin@s," but I liked this clue anyway.
3. Worthless weather starting in Hoenn... and in Leningrad! -- &Lit, Acrostic
The first &Lit clue of the puzzle! Hail is a crummy weather; in Pokemon you'd first find it in Hoenn, but in real life it might be found in Russia. For the extraction part, the starting letters in "Hoenn and in Leningrad" give us HAIL.
4. EA Kart characters might be found in the Fighting Dojo (KARATE) -- Anagram
Not for the only time in this puzzle, I wish I could just use the Japanese name for a trainer class (Black Belts, in Japanese, are just called "Karate"). Karate might be found in the Fighting Dojo, of course, whether or not it's the name of the guys there. EA Kart characters rearrange to make KARATE.
5. Joint goddess of the night in disarray: she had a controversial makeover (JYNX) -- Anagram, Charades
A joint is a J (for some reason I don't think this is a "standard" cryptic abbreviation); as Phoopes noted Nyx is the goddess of night, so putting her in disarray gives us YNX, with a leading J for JYNX. Jynx, of course, had probably the most notorious redesign in Pokemon history.
6. Heartless Kanye vinyl given out by Skrelp (KELP) -- Abbreviation, Charades, Deletion
A "heartless" Kanye would be KE (Kanye without the middle letters). Add onto that a vinyl record (LP) and get KELP, which is dropped by Skrelp in Gen 9. I've never played ScarVi, and the TM material items are basically impossible to find information about if you don't know
where to look, so I'm lucky I was able to find this.
7. A young adult is in sight for a feminine fruit (STEENEE) -- Insertion
Put TEEN (a young adult) into SEE ("in sight") to get a feminine fruit (STEENEE).
10. Steer, out East and astray: get some sleep (REST) -- Anagram, Abbreviation, Deletion
Steer without one of the Es ("out East") is Ster; astray tells us to rearrange it and get "some sleep" (ie, REST).
13. Backwards bogeyman beheaded baby bug (Snom) -- Deletion, Reversal
A bogeyman is a MONSTER; cut the head off to get MONS, and flip it backwards to get SNOM, a baby bug. I'm a sucker for the alliteration clues.
14. Gliscor gets tricked by mixed fruit! (PECHA) -- &Lit, (Indirect) Anagram
Peach is a fruit; mixed (rearranged) gives us PECHA. Gliscor sometimes gets lured by mons with Pecha Berry and Trick, which gives us the definition. This is an indirect anagram, and I worried about including it; but I felt the limited number of five-letter berries, and the on-the-nose &Lit definition made it pretty gettable. I was really excited when I came up with this clue, ngl.
15. At first, radishes, oranges, or tulips make for a big plant (ROOT) -- Acrostic
A "Big" plant would be the humble Big Root; taking the first letters of "radishes, oranges, or tulips" gets us there.
16. Gutted saltwater fish can help with focus (SASH) -- Deletion
A Focus Sash can help Pokemon with focus; taking "saltwater fish" and gutting it (removing the middle letters) gives us SASH as well.
18. Posh roommate conceals a baby dinosaur without its tail (SHROOM) -- Extraction
For the definition, a baby dinosaur (SHROOMISH) without its tail (SHROOM) -- this technically contains some wordplay, but "Shroom" isn't a Pokemon so cut me some slack. "Posh roommate" conceals (has the hidden word) "shroom" in the middle of it.
19. Fearmonger blended Oran (ARON) -- Anagram
Oran, blended (rearranged) is ARON, a pokemon known for its FEAR strategy (ie, a FEARmonger)
21. Tiny bird's wild tuna (NATU) -- Anagram
Natu is the Tiny Bird Pokemon, which is also "tuna" rearranged
23. Isopod dishonorably hides a little weed (ODDISH) -- Extraction
Another "hidden word" clue: "Isopod dishonorably" has "oddish" in the middle. For the definition, Oddish is of course a little weed :)
25. A science class ends up crouched near mouse automaton! (NERD) -- &Lit, Acrostic
I am very proud of this one! Super Nerd is a "Science" class (a science-related trainer class -- in Japanese they are actually just named Science). Taking the ends of "Crouched near mouse automaton" (DREN) and putting them up (ie, in reverse) gives NERD. Put all together, "A science class ends up crouched near mouse automaton" is also a description of the Super Nerd's sprite in Heart Gold and Soul Silver!
26. Warm ends of eel lead to ancient king's final abode (HOTEL) -- Charades, Deletion
A synonym for warm (HOT) and the letters at either end of "eel" (EL) put together give HOTEL. Recently-released Pokemon Legends ZA features AZ, an ancient king, running a hotel, where Bulbapedia tells me he intends to live for the rest of his life.
27. User experience before Internet Explorer 4's model of acuity (UXIE) -- Abbreviation, Charades
User experience (UX for short) combined with Internet Explorer (IE) gives us UXIE. "4's model of acuity" is the definition: Uxie is the Gen 4 Pokemon that lives in (and embodies) the Lake of Acuity. I went through so many bad clues here before I landed on this, and I'm glad I ended up with something this good.
29. Initially acclaimed, someone overreacted regarding the primal games' unusual nickname (ASOR) -- Acrostic
The starting letters ("Initials") of "acclaimed, someone overreacted regarding" give ASOR. The "primal games" (games with the primal Pokemon -- Omega Ruby and Alpha Sapphire) are normally called ORAS, but once in a blue moon you see ASOR. It's certainly unusual! I'm not happy that I had to include this word, but I needed SOMETHING to cross there, and Bulbapedia has a redirect for it at least! "Unusual" could be wordplay suggesting to scramble ORAS, so I guess that's also an angle.
30. Cut-off old flyer to make music with Smith (AERO) -- Deletion...?
This is a weird one -- the definition here is "Cut-off old flyer" (Aerodactyl is an ancient Flying-type; cut off the end to get AERO). Aero, put next to Smith, gets us Aerosmith -- ie, it makes music. Now that I look at this, I think I originally had "makes music" instead of "to make music," and that was absolutely better.
32. Ghost-fighting ability is the number two thing in recon (SCRAPPY) -- Insertion
"Ghost-fighting ability" is a very on-the-nose definition for the ability Scrappy. "The number two thing" is CRAP, and if we put that in a synonym for "recon" (SPY) we get SCRAPPY.
33. Rain, snow, and hail heal him; shirtless sleet is surprising (SEEL) -- Anagram, Deletion
As Phoopes more or less identified, Seel is a Pokemon that gets both Ice Body and Hydration, which means it can be healed by Rain or Snow/Hail. Gotta include sleet for the USPS slogan, and here it gives us the wordplay: "Sleet" without a T (shirt) is SLEE, which we can rearrange ("surprising!") to get SEEL.
35. Short, clueless alien tells you the scale (CLEF) -- Double Definition
A clef, in music, tells you the scale of the staff it's on. Clefable is a clueless (Unaware) alien (they're from the moon!), nicknamed "Clef" for short.
36. Brock's mother in an exotic form (ALOLAN) -- Double Definition
Brock's mother, in the anime, is Lola; "Brock's mother in an" means we insert LOLA into AN to get ALOLAN. An Alolan Pokemon is an exotic form of a previous gen's Pokemon. I wish I had something better to get to Alolan here. I guess it doesn't really need to be a Pokemon thing. Maybe I should just put another musical artist in there or something.
38. For starters, I'd say leading Excadrill is key for Klara (ISLE) -- Acrostic
Taking just the first letters (starters), "I'd say leading Excadrill," gives us ISLE. Another word for an isle is a key, and Klara is found on the Isle of Armor, so an ISLE is a "key for Klara."
39. A champion's Christmas carol is coming up (LEON) -- Reversal
Leon is the Elite Four champion in Gen 8. Another word for a Christmas carol is a noel, and coming up tells us to put it in reverse.
41. Grow, heat, or coat starters above (OVER) -- Double Definition
Overgrow, Overheat, and Overcoat are all Pokemon words, and "Over" is the starter for all three of them. Likewise, "above" is a synonym for "over."
42. Chateau's noble class is real queer (Earl) -- Anagram
Our last trainer class clue -- the Battle Chateau features a trainer class named Earl (in addition to Barons, Viscounts, etc -- all titles of nobility). We can rearrange "REAL" to get "EARL," with "queer" as the anagram indicator.
43. Treetop alcoholic has an elderly boss (OPAL) -- Extraction
"Treetop alcoholic" has the hidden word "OPAL" in the middle; Opal is the name of an elderly Gym Leader in Gen 8.
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