They really shouldn't be compared. If I had to choose, I'd pick FRLG.
Ruby and Sapphire are far better because of innovations and side quests. FireRed and Leaf Green are good because of the nostalgic feelings.
I actually like R/S/E better(especially emerald) becaause of new and superior storyline, and the battle frontier in emerald.
I really need something to put here.
Each game has it's pro's and con's and depending on what you're looking for, it can affect which you think is a better game although I'd say Ruby and Sapphire are marginally better than Leaf Green and Fire Red.
Hoenn was less cluttered and had more areas to explore. It also had the new feature of Diving. Plus the story-line was much more gripping and despite the post game development, you could make your own events through contests and secret bases.
I like R/S/E better. It has battle graphics and some cut scenes
Every other cast member > Clemont/Bonnie
I would pick Firered and Leafgreen, to me FR/LG feel a bit more brighter and polished. Ruby and Sapphire are still fun to play, but I prefer Firered and Leafgreen.