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Gonna go ahead and take remakes out of the equation, as well as Gen 6 because it just started.
5 > 4 = 2 > 3 > 1
B/W1 only having Unova Pokemon was a great idea, and it made everything feel more fresh. All three of your rivals were good, especially N since he was so unique compared to the rest. The yin-yang theme was a really good idea and is pulled off pretty well. There were also a lot of nice little polished touches such as seasons, reusable TMs, combined PCs and marts, etc. The gym leaders actually gave a fuck and got involved in the plot. B/W2 was even better; while the plot did take a hit, it made the gameplay even better with 300+ catchable Pokemon in-story, challenge mode, and the fuckin' PWT which is every fan's dream come true.
4 and 2 are about equal for me. Gen 2 might be the most important game in the franchise when it comes to additions, but the neutered Kanto, shit level curve, and most of the interesting Pokemon being available only in post-game brought it down. Gen 4 added some very great features, and had the best villains, but I thought the Sinnoh region itself was pretty lame, and I disliked most of the Sinnoh Pokemon.
3 had a strong early game and mid game, but weak late game. The rivals and the villains were both shit, too. On the other hand, abilities, natures, and expanded EV system were all great additions, and I've clocked more hours in the Battle Frontier than GSC's shitty Kanto.
1's the worst. It's not bad at all, but it has the least features and is kind of clunky to play, which makes sense, because it was the very first Pokemon game. The only things I'd say it really has over the other games is Blue/Gary and the fact that Kanto's slightly less linear.
