If you are wanting hacks many and plenty then I would have to point at the DS version of 5. I have not looked at it since I figured out how to undub it (I think I had to rename something or look in a different directory) and in doing so setting me on this long and dark path of being a ROM hacker, however fiddling with file systems is far
By all means look at the GBA versions too as I am also not such a fan of some of the things they were doing in later versions to make them the tiniest bit different to what came before, however for pure ease of hacking, tool making and fiddling then DS version of 5 surely has to be it.