I, personally, didn't enjoy Fire-Red, or Leaf-Green. Not because they weren't good additions to the Pokemon franchise, which they were, but because I felt I kept getting a feeling of nostalgia, and not the good kind either. More of the 'I've been here, I already know what I have to do, can we just get this over with already?' kind of nostalgia. Fire-Red and Leaf-Green both had their good points, but, to me, I felt that they were the worst versions in the series. I just didn't feel the spark that I did when I first picked up Pokemon Red and plugged it into my Gameboy Pocket. The rush was just... gone.
HeartGold and SoulSilver however, is a different story entirely. I didn't really appreciate the female lead changing, since I felt that that changing it was taking away from the memories and idealistic fantasies I had about the Gold and Silver remakes. I always imagined Gold, Kris, and Silver in 3D, running around Johto and Kanto. Instead, I got Gold (or Jimmy, depending on who you ask), Lyra (or Kotone, once again, depending on who you ask), and Silver (who's history was actually explained this time). The nostalgia was there in HeartGold and SoulSilver, but there were enough changes to make the experience fresh. From having a Pokemon follow behind you (a throwback to Pokemon Yellow), to chasing down the Legendary Dogs, to battling Red atop Mt. Silver. Every memory from my childhood was brought to life in HeartGold and SoulSilver, and they brought friends.
I think HeartGold and SoulSilver were the best games of the 4th generation, just because I didn't feel like Diamond/Platinum/Pearl were really adding anything to the series as a whole. Yes, some new Pokemon, along with new abilities, were added, and (obviously) everything was in 3D, which I felt was a big step in the right direction with Pokemon. But, in the end, to me, it just felt lacking of something. Platinum didn't change much from Diamond/Pearl, besides the Competitive Meta-Game, move accuracy changes, 'formes', and the Lost Dimension (which I nicknamed the Negative Dimension).
So, in my opinion, this is the list of how the Pokemon...
1.) Pokemon Red/Blue/Green/Yellow
2.) Pokemon Gold/Silver/Crystal
3.) Pokemon HeartGold/SoulSilver
4.) Pokemon Diamond/Platinum/Pearl
5.) Pokemon Ruby/Sapphire/Emerald
6.) Pokemon Fire-Red/Leaf-Green