Hey, Lioncash, you have free reign to take the project wherever you like. I've been trying to diffuse the idea that this is "my" project.. I really want it to be a community effort. So anyone with programming experience that has an idea for the project and wants to run with it, let me know and I'll give you access. Obviously there will need to be some type of coordination between everyone working on the project at once. As for me, I'll be working almost exclusively on the natives for the foreseeable future (the next couple of "big updates" are removing the SDL layer and restructuring the project to match the original Mupen64Plus and make it buildable for multiple targets), so changes to the GUI front-end shouldn't interfere much with what I'm doing.
Like I mentioned before, I've been focussing on my commercial app for the past few weeks, but it is getting closer to completion (it's about 50% - 66% of the way complete), so I'll be getting back to focusing primarily on Mupen64Plus AE soon.