The main problem I have is that if I load a save to go anywhere in Hoenn, the game becomes buggy and my party becomes eggs. It works fine, if I restart a new game, but I cannot visit all places for testing.
The problem about saves is because the engine moves the data around so you can be sure as heck that it will probably turn every caught Pokemon in an old save file into bad eggs. So can't do anything but restart your game.
It's because of an old feature that was inserted into it. I actually mentioned it in the main post. To get rid of this, open bytereplacement file and get rid of data following "negate pokemon encyption" and your saves will work just fine.
Furthermore, the new move table is terrible because torchic and mudkip have ember and water gun at level 5 and it is impossible to defeat May's mudkip with a torchic.
You can just edit the trainers using a trainer editor, so they won't have those moves at level 5. :P