I think you tried to do too much at once and it got complicated. I know making a hack is not easy and it requires a lot of work. Maybe try to keep it a little bit simple. Dont try to add too much at once. Have a core story and set of maps with reasonable healing points and access to pokeballs early and I think it will be a much more enjoyable game.
Im not trying to be mean, sorry if it seems that way, im just giving my opinion and advice. Thank you for actually taking the time to make the hack.