I like FRLG better than RSE. After GSC, Ruby and Sapphire let me down because they didn't include all of the Pokemon (and as Blastoise was my favorite Pokemon, I was upset that I had no way of obtaining one until FRLG came out), weren't backwards compatible, and only included one region. I suppose after GSC, I expected new games to continue the trend of allowing trades with previous generations and letting the user explore the regions present in previous games, so I was surpised when neither Kanto nor Johto was present in R/S. I've also never cared too much for water in Pokemon regions, and Hoenn's abundance of oceans didn't sit well with me. Overall, the Hoenn games have always been my least favorites, and I think a lot of that stems from the fact that they followed my favorite games and didn't live up to the same expectations.
By contrast, FRLG brought back many of the Pokemon I loved, and allowed me to explore Kanto all over again, which I loved. Also, when I first played Red, most people I knew used the Missingno glitch all the time, and I liked the idea of playing through an expanded Kanto region without the same glitch issues present in RBY. Unlike with R/S, I knew what to expect when I bought LeafGreen, as I'd played most of the game before in the form of RBY. Consequently, FRLG lived up to my expectations better than RSE did, and as a result, I continue to prefer the Kanto third generation games to the Hoenn ones.