First off, thanks for the feeback, but I'm afraid I'm going to have to disappoint you here.
I write things the way I do to try and cut down on the work I need to make this game, the extra changes you've talked about would all mean a LOT more writing and in some cases coding for me and that's just not what I want to do.
The main priority for me when making this is that I have fun doing it and if it becomes too much work, then I stop having fun and the game would never get updated.
Like making Heatran a pure girl and not a futa, that means twice the writing every time I try to include her in a scene, it's just not worth it for me to put in that kind of effort.
One thing you suggested that I will do however, no Mon is getting more HP than Arceus, not unless there's a story reason for them to have that much, which there usually won't be