Personally, I liked FRLG better. RSE have grown on me in retrospect (well, Emerald is still a lot more appealing than the other two), but the nostalgia factor induced by FRLG added a lot for me.
Of all of the Pokemon games, I found R/S the most disappointing on release. Sure, they were good games, but I really wasn't ready for a reboot of the series, and after my favorite game (Gold), they felt like a step down. They also cut off access to many of my favorite Pokemon (including Blastoise, my #1), leaving me with alternatives that I didn't like as much. (Perhaps the reason why I liked Emerald a lot better is because I was able to trade in some of the inaccessible Kanto and Johto Pokemon, and therefore was able to mix my old favorites with my top picks from the Hoenn contingent.) FRLG, on the other hand, rectified the things I didn't like about Ruby and Sapphire. They brought back my favorite Pokemon, and allowed me to explore one of my favorite regions again (vs. Hoenn, which I didn't like as much), reliving my childhood memories from my earlier playthroughs of Red.
Could FRLG have been better? Yes, but so could RSE. The games could have had more content, etc. Emerald improved in this regard, but since I'm basing my verdict primarily on the first two games of each set, R/S come up short for me. If they had come at a different point in the series' history, I might have liked them better. But as it was, R/S were a step backwards, in my opinion, and FRLG stepped back in the right direction. (Emerald had the awesome Battle Frontier, but it was in Hoenn, which I don't like as much as a region, so I guess it comes in somewhere in the middle.)