Of course, most of these are just mentioned because I like to speedrun games, but here are some suggestions you might want to add to the game to make it more unique from the original series and rom hacks.
1) Release Pokemon From The Party
Rather than having to go all the way back to a town and use a computer, why can't we just release them directly from the party in the wild? If you add this, I'm sure it'll help a lot of people who want to be on the go.
2) Super Randomizer
Randomizer is great, but why not also randomize every item as well or do variations of the randomizer, such as "Gotta Catch 'Em All Mode", which makes it cycle through every single pokemon everywhere until you can literally catch all of them sooner, rather than later.
3) Legendaries Must Stay Legendary
Truthfully, I hate the idea of being able to tame a Legendary Pokemon, it defeats the purpose of them being Legendary to begin with. Like, if everyone can capture them, then what's the point of them even being Legendary? Like, I get people may be after the "catch 'em all" achievement for personal needs or whatnot, but it truly makes no sense for a Legendary Pokemon to be easy to capture (for the most part) if everyone can capture it. If they were really Legendary, they would be nearly impossible to capture or you should limit it to a much much much harder difficulty to capture them.
4) Improved Shops
Some items would be nicer to have earlier on (despite their price), such as EXP Share. I really don't want to almost beat the game to finally get something to help my team out.
5) Better Randomization
Randomization should be fixed, it seems to be extremely broken and making the game not only NOT difficult (even on the hardest difficulty), but pathetic nonetheless. If anything, the randomization should be based on area, such as all water Pokemon being available only in the water, all snow/ice pokemon only available in the snow, grass in grass, poison/dark in caves, flying in the mountains, etc.
6) Avoid Trainers (+No Story Mode)
Once again, the biggest issue I have with Pokemon games is having to fight trainers, rather than being like "nah, I'm good, I'd rather just capture pokemon". Truthfully, I don't care about the story in this game (or any pokemon game, since they're always the same thing over and over again, never really original). So perhaps, could you add another mode that removes the story and just lets you explore as a NPC and capture Pokemon or something.
7) Broken Move Fixes
Sometimes in the game, certain moves (despite what Pokemon you are using and they are using) break to the point it doesn't even make sense. Like, I was fighting a Hiker in the first cave with a Gastly and he was still able to use "Tackle" on me, despite that move not even being possible to used on a Gastly.
8) Updated Animations
Many animations are the same thing and tend to make the game pretty bland when a Fire move doesn't actually show fire or a water move not actually showing water. Truthfully, around 20 or so moves all share the same attack animation against the enemy as "Tackle".
9) Game Editor
One of the biggest issues for many people is being unable to edit the game ourselves, we sit around waiting for others to fix or modify a game that we would like to be modified already. Perhaps you can include some VIRUS FREE programs (this means scan them with VirusTotal, MalwareBytes, etc) so that we can edit the game ourselves and share our "edits" with others.
10) Move Tutor 'N' More
It seems you have the Move Deleter and Name Rater available early in the game, yet not the Move Tutor? Fix this perhaps...