In order of preference (not counting Black/White):
Red/Blue/Green > Gold/Silver/Crystal > Yellow > Diamond/Pearl > Platinum > HeartGold/SoulSilver > Ruby/Sapphire > FireRed/LeafGreen > Emerald
I like the R/B/G arc best mainly because it provided the best Team Rocket story ever, which went from a subplot like in the games and then wound up taking over the main plot, and was very suprising in it's complexity. Red, Blue, and Green were also all great lead characters, and the side characters (Professor Oak, Bill, the Gym Leaders, etc.) were all done perfectly. It was great.
G/S/C, Yellow, D/P, and Platinum are all great arcs (though Platinum still has yet to finish, the two volumes it has are awesome), and from what I've seen of HG/SS, it's good. I did not care for the Generation III arcs though. Ruby and Sapphire were annoying leads, the villains were noticeably weaker than what we've had before, and Groudon and Kyogre's fight went on
forever. There were multiple flaws in FR/LG's story, and the character of Emerald singlehandedly dragged his arc down to being the weakest (it wasn't exactly
bad, the Frontier Brains were awesome after all, it was just....weak. Weak hero, weak villain, generally weak storyline.)
Honestly, I love Crystal as a character and if you ask me, the sudden switch made me wonder what happened to Gold and Silver and what Kusaka was planning. So I waited two volumes of enjoyable stories of Crystal and eventually, Gold and Silver returned in a pretty cool plot twist.
Indeed, Crys was awesome and the wait for Gold and Silver's return helped build great suspense.
I really wasn't fond of the Hoenn Frontier Brains. They all seemed like jerks. Especially Brandon and Tucker.
OK, you may have to reread that arc; they were jerks to Emerald because he was a jerk to them
first. He assaulted and tied Tucker up when he first arrived, for Arceus' sake, so Tucker was
more than justified in despising the little twerp afterward.
And they
all seemed like jerks? How is Greta a jerk? How is
Spencer a jerk!?