3rd Gen has been growing on me. R/S really pissed me off when it came out because I was so disappointed you couldn't go back to Johto or Kanto, and because so many of the Pokémon were missing (along with the lamentable loss of the clock function). I played through Sapphire and beat the E4 but never really got into it as much as I had the previous two generations. When Emerald came out I gave it another shot and found it to be much better; the previously mentioned two issues still irked me, but there were a lot of improvements made upon the series IMO between G2 and G3 (i.e. Natures, abilities, new moves, general aesthetics, etc.), and I liked the setup of the cities and towns in the region (Fortree, Sootopolis, and Pacifidlog had more interesting setups than any town/city in Kanto or Johto). The Pokémon, including the legendaries and especially the starters (aside from Blaziken, who is the only one awesome enough to hang with the previous starters), were still not as interesting, and I kinda missed Team Rocket (wish they could have had them in there as well as the other two teams--it might have been crowded but they could have expanded the game to incorporate them, and it would have been more interesting), but I was starting to get to know them better, and in Emerald the two teams got interesting because you got to battle both of them.
FR/LG were both great games; I was disappointed at first because I had been under the impression that it was an entirely new game set in Kanto, rather than just a remake, but, again, it grew on me. Love the Sevii islands addition (although they should have added the Orange Islands from the anime), although they were a little too short for my liking, but it was cool playing through FR/LG with the upgrades G3 had been given...something that G2 is sorely lacking. I'd still take my Crystal over LG or Emerald any day, but it'd be sweet to have these other improvements in that game, as well.