Well, after a bit of an adventure downloading and installing Ubuntu, I was able to run the builder program. It worked great, and didn't take too long even in a VM. I especially liked the little counter-spoiler option that hides filenames, that was a nice touch.
As for the port itself, it looks fantastic! When I first started it up, it seemed to run even better than my macbook. It wasn't until the dream sequence with all those enemies that the frame rate dropped enough for me to notice it. I got to Naija's home ok, and in there it runs like a dream. It crashed and shut itself off when I tried to reenter home waters, but when I relaunched it it worked ok, so no reproducing that bug, sorry. Home waters is a bit choppy just because it's so well populated, but despite that it's just as awesome as when I first played Aquaria. I can't believe that my PSP can do this, it's just amazing.
An engine rewrite sounds like a lot of work, but I'll be first in line to try it out if it happens! Maybe it can be integrated into the PC versions, too... my first-gen macbook plays the game well for the most part, but it still slows down in some parts. Maybe that would enable ports to other platforms as well, like the Wii or Android or the iPhone.
In any case, thanks a ton, achurch! This is so cool.