I'd say Emerald for the Battle Frontier alone.
Now I could go on about why I like Emerald the most, but instead I'm going to say why I don't like the others as much.
One reason is the version exclusives. In most games, I feel like I'm really missing something. For example, out of FireRed and LeafGreen, I prefer the exclusives in LeafGreen, but I still feel like I'm missing out on some of my favourites like Golduck and Cloyster. When I play Ruby or Sapphire I don't feel like I'm missing much at all. However in Emerald, I feel like I'm missing out on Medicham and Roselia, which are two Pokemon I'm rather fond of.
Second is how the games just stop after the Elite 4. This was acceptable in Red and Blue, but not Third Gen. I mean come on Second Gen gave us the chance to re-explore Kanto, plus battle Red, the strongest trainer of all. FireRed and LeafGreen had the Sevii Isles plus the revamped Pokemon League. In Ruby and Sapphire, all you get is the Battle Tower and Sky Pillar.
Lastly, is the stories all feel like the same thing. It's kind of hard to describe, but to me it kind of feels like Emerald's the book and Ruby and Sapphire are the movie. They tell the same story, but Emerald is MORE the story. Ruby and Sapphire feel like Emerald with cut corners. It'd be like in the book(Emerald) Wallace is the supposed last challenge, but the Steven comes along bigger and stronger. So in the movie(Ruby and Sapphire) - to save on time - they made Wallace the last Gym Leader (which is LIKE the last challenge), but the you get to the Pokemon League and there's Steven, still the last hurdle. Also in Emerald the whole Team Aqua/Team Magma thing in more complete. I doubt this is making any sense, but basically to me it feels like Ruby and Sapphire are the movie to Emerald's book.