Oh darn, now I feel real bad for VGAura and Megiddo, because I still think that that hack right there in the middle outclasses the other two, that being Pure Gold.
The most glaringly obvious reason that I vote for Pure Gold is the extensive use of assembly editing and hexadecimal editing that has gone into some pretty minor - and, of course, major - details of the game. I think Zodiac really executed the FireRed-style emulation, what with the great tile insertion, font editing (including things such as the menu), right down to things like the titlescreen's style. Speaking of the titlescreen, I think it - although the Ho-oh sprite could've been a better choice - is really nifty that Zodiac managed to animate Ho-oh. I have to admit that the headbutt trees' tiles could be better, and so could the semi-long grass tile, but that is being slightly picky.
Identity didn't get my vote again, not only because of the reasons I mentioned before - the player speaking, the elusive lack of... something - but because it doesn't seem to have made any progress at all since January; or at least public evidence. I know that is kind of assumptious of me, but I just think Identity doesn't take the cake on this one. I also seem to have lost interest with the story now - it just seems that the more I read it, the... weirder it gets - I know that VGAura wasn't aiming for an exactly ordinary story, or at least that's the impression given, but I still think that the idea is straying a bit too far into the corners of Pokémon that, yes, they haven't been tinkered with, but also don't need tinkering with. Yeah, most of what I'm saying is contradicting what I said last month, but my opinion seems to have changed. Sorry, VGAura. Identity isn't bad, it just isn't good enough, for me, to get my vote.
Now, Top Secret. The story has a lot of plotholes. The palettes aren't the best. The mapping is good. The scripting, or at least of what I've seen, is great. I just don't like it. The atmosphere given off by the screenshots etc. just... don't exactly scream POKéMON! to me. :/ Megiddo is a good hacker, but I'm afraid I just don't like his hack. Sorry. :/
So yeah, my vote goes to Pure Gold.