I would know if there is a way to edit, or better, remove pockets from the bag. Example: how can I remove the "mail" pocket or shift the "battle items" pocket into another (for example the "medicine" pocket)?
To change the order of pockets, just open the script called Settings. Somewhere in there is a list of pockets and things that go with them. If you just want to reaarange them it shouldn't be a problem. Just make sure you change the lines around them so it still works.
Like if you change where the berry pocket is, make sure you also change the line below that talks about the berry pocket.
It shouldn't be a problem to remove a pocket, unless you still want that kind of item in the game.
Yes, changing which pockets exist in the game is easy (edit the array in Settings, and make sure the couple of other settings there are accurate). The hassle comes when you also need to edit items.txt to move each item into the appropriate pocket, and edit various graphics to suit the new arrangement of pockets.
Off the top of my head, the graphics that need changing are the various Bag ones in Graphics/Pictures, plus the pocket icons in the folder Graphics/Icons with the names bagPocketX.png.