Ooooh this gonna be good. Here's some ideas I have:

A couple serious ones: Super Easy, 50k and 99,999 points (or whatever the score limit is in that, if there is a lower one). Could do 2D and 3D. Maybe even another if the score counter in Super Easy goes higher. IIRC, the GBC S-Easy mode capped at 9,999, so my memory is real fuzzy on this. Gary2 & Mewtwo V/S-Hard x5/x10: Just have a save file at Gary2 on V-Hard and/or S-Hard, and beat both him and Mewtwo 5 (or 10) times (total 10/20), resetting the console/emulator after beating Mewtwo (for practice, maybe) Final Stages%: 1P stadium, have a save file on each of the final stages, and play through just those (including Mewtwo on V/S-Hard, of course).

Now the goofy ones: "I'm feeling giddy!%": 1P stadium, any difficulty, play until you get to Team Rocket, and stop the timer when James says the famous line. No beating Team Rocket before James says the line. "ForkyStrats" / "x8+ chains only" / "Violence only": 1P stadium, any difficulty, either get a mystery chain on each stage in the run (or maybe just x8 minimum instead of x15), resetting the run/stage if a smaller chain happens before the stage ends. I'm just thinking of some high value for the chain, so definitely open to this being tweaked. Waifu%: 1P stadium, have a save file on any non-Easy difficulty at Lorelei, play through her stage 10 times, resetting the console/emulator upon clearing, and going back to the save file again. Only came up with this because of people... calling her Waifu in chat (can't blame peeps), and thought of the Lakitu% run for TA. Bulbasaur/Squirtle%: 1P stadium, just pick Bulbasaur or Squirtle for each stage in the run. Accidental other Pokemon selection just needs a back out, no total run reset.

I don't know how I want to classify this one, but: Marathon, combos only: 50k/99,999, just make combos, no chains allowed.