The core gameplay is already fine as it is right now, an argument could be made about balancing, but I'm not that interested in that, since it's a fangame and you're probably a solo dev. Perhaps it could be interesting if there was a way to colaborate with you via github or something similar? I don't even know how you already have so many pokémon and trainers done, that must have been a lot of work.
I only miss some QOL stuff, like: A pokédex where we can see pokémons we obtained and their moves; Perhaps which pokemons are available for each gym leader (since I noticed the shop rotates the same pokémon) to plan better for the champion; Maybe a similar thing to pokédex, but for trainers you already defeated with their teams; Or even for the random events you watched, like the crossover stuff and battles events involving 2 or more trainers, possibly even in the form of achievements... Stuff like that.
I understand all of those take time to develop, specially if you're new to coding (and I don't know if that's your case), that's why I asked about it going collaborative. This game has a lot of potential and I could see a future where a huge community plays it regularly.
Either way, great job. I'll try the SMT one sometime later, since I like that franchise as well.