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There's a difference between best and most fun.
Best is Ash Gray. Tons of clever applications of JPAN's Fire Red Hacked Engine, intricate scripting, and painstakingly difficult utilizations of the of the OW, among other things. However it's definitely not the most fun.
Most fun that I've played might have been Snakewood, even though it wasn't really that "academically" good. The best "golden median" one I believe would be Sienna. Flora Sky is high up there too.
And things like VW/BB or Fire Red Omega are barely hacks and shouldn't be counted as such. They're game edits to give more substance to the catching/battling component of the game, done relatively easily with one or two rom editing programs. There's nothing wrong with that, but I don't think they can be classified the same way that full-fledged total override hacks that take a holistic knowledge of the rom structure are. Regardless of which one you like more, they're not the same thing.