I've only really noticed this hack- well, not so much notice as remember, haha. And wow, I'm impressed! I've only played a bit of the Golden Sun series, but it's certainly a unique one, and to bring it together with Pokemon has proven to be a great idea. I've played a bit of the alpha, and while there are a few things that irk me, such as blankish mapping, a few tile errors (and some of the tiles themselves, to be honest). But otherwise, this is a very solid idea you have here. I especially love the smaller edits you've made- they've really contributed to making the hack unique. For example, the animated sprites, the new music, and ESPECIALLY the fact that you even changed the sound made when you select something. I'm probably going to be PMing you sometime asking you how you did that, haha :P
Great work so far, keep it up!