HeartGold/SoulSilver.
I loved the originals back in the day, but looking back past the nastalgia, they were horribly buggy, slow, painfully boring once you beat the Elite 4, and kinda bad. The differences over the generations each stack ontop of eachother, so going backwards just feels wrong.
Ruby/Sapphire/Emerald/FireRed/LeafGreen made awesome strides by modifying the underlying mechanics of the game, making it appear unchanged for most people, but extremely open to people who wished to dive deeply into the game and its mechanics. Abilities, IV's (0-31 instead of 1-15), Items (new berries, new hold items, etc) and moves made the third Generation extremely dynamic.
The fourth Generation, consisting of Diamond/Pearl/Platium/HeartGold/SoulSilver polished over some of the jagged edges, and incorperated 2.5D Graphics and online play. The physical/special split let the individual moves decide if they were effected by Attack/Special Attack, rather than there typing: making some useless Pokemon useful.
HeartGold/SoulSilver was my favorite because it was LOADED with new and old Content. Back in the day I loved Gold/Silver, and this was what a remake should be: a perfect mixture or new and old features, a fresh new game with a twist of nestalgia.
I did buy White version, and so far, its... different. Im not far enough in to tell if its a good different, or a bad different. You can only build so far before you run out of space to improve, and Pokemon appears to be hitting that mark. This game felt like more of a game for competitive people, giving them more edgy moves to put into their toolbox (so, ya know, not every team will pack an Earthquake...). Its fun, one of the best yet, but the changes make me feel underwhelmed.
I think after the third version of B/W, the only place the series can go without stagnating is to an MMO setting.
Which I wouldnt mind...