I agree that HGSS is the worst to play a challenge on. Having access to all the Pokemon is nice (and I didn't have a problem with his Dragonites) but there is too much grinding to be done for Red. I haven't beaten HGSS yet. My original playthrough, I beat the E4 the second time, but halfway through training for red, I gave up because it was so boring. Now I'm to the Kanto part (I think) of my Water Monotype.
Best game is RB fo sho. Sydian doesn't know what he's talking about at all. I know if I look at the challenge and say "would I rather do a _______ monotype on Blue or Ruby?" it will always be Blue. Sure you don't have access to as many Pokemon, but you don't need access to as many Pokemon. Plus the insane speeds it can run at.
I think my rankings goes: RB (I don't ever include yellow because it is just different, and I think in general challenges are easier on R/B and yellow is never in a different category) -> RSE ->GSC ->gap since the rest are so inferior ->DPPt ->FRLG ->HGSS.
I don't like FRLG at all. IMO they are much harder than RB even with access to more attacks and more Pokemon. Plus you have to do extra storyline, can't run it as fast, etc. If I am ever given "beat a challenge in Kanto" it will always be R/B, not YFRLG, and if I am ever given "beat a challenge in Johto" it will always be GSC, not HGSS. The only reason I am doing a HGSS challenge right now is that I'm not contempt with the Water UMC title, and am beating the rest of the games as well.
Tl;dr Red/Blue are god tier, RSE and GSC are good, the rest are awful.