To me, Turquoise is one of the few gems out there that doesn't get half the attention it deserves- the selection of graphics are nice and flowing, the story is solid, and it's just enticing overall.
However, Identity and Flora Sky also have unique features. For starters, Identity has a great plot, which makes it really fun to play. Flora Sky obviously has the best graphics, but... I found it a bit too much like Light Platinum- in that it uses the latest graphics from the official games, those considered "cool". While the graphics are impressive, I felt the story needed work- I remember playing the beta, and the first Gym Leader...
Literally, he said "Hi, I'm [name]. Let's battle now!". And, simple as that, the battle began. In my opinion, the game needs more depth. Maintaining good graphics are fine, just don't neglect the other aspects.
While saying that, I think Identity should give a little attention to the graphics. Sure, it can be concluded that tiles are unimportant, at the end of the day- but frankly, since Azure Horizons popped up, many people are just using the default FR tiles. They're now overused, so.. For a bit of diversity, VGAura should consider working on graphics.
Now, back to Turquoise. It's got a great balance between a decent, classic story, and custom graphics. It would seem Tropical Sunlight is a talented scripter, too. Therefore, and sorry for the really long post- Turquoise gets my vote.