Gold and Silver, I'd say.
I started with Yellow, and moved on to Red/Blue. And they were good, everything was novel, and I learned what a Pokémon game was about.
Then Gold/Silver came out. An entirely new region filled with old favourites and interesting new Pokémon (and some stupid ones, of course - I've never like Unown, for one). It was a different story, but a continuation to the previous generation. There was a bit more to do and see (Headbutt/Whirlpool/Bug Catching Contest/etc.), but not so much that I felt I was being bombarded by it all. And on top of all that, Kanto was in there as well! True, it may have been shrunk a little, but little of value was lost, and much of it was modified so that it was all new again.
For the time, Gold/Silver were the best. Ruby/Sapphire were certainly good too - they improved the story part of the game, introduced new dynamics to raising Pokémon and so forth, and of course had better graphics. They come in at a close second, and I suspect the dislike was mainly (solely?) because of the lack of compatibility with the older gens.
I like the retro feel of the early generations. It was simple and clean, and not cluttered up with contests and ribbons and Undergrounds and Battle Towers and all that nonsense (most of which I never looked at because, I'll admit, I used ROMs). The minimal story was good, because it allowed you to explore a little and it only gave you a vague prod in the right direction. The story nowadays feels far too imposing, and far too much of it paints you as the friend of all living things, the Mary Sue hero in this very nice world that's somehow troubled by those two Team Generic grunts standing at one of the town entrances. When Team Rocket took over Goldenrod, they were all over the place and the townsfolk had gone. It's just not the same.
I'm not considering the second gen remakes in this, partly because I haven't played them (my ROM crashes after 31 events, and it's horrible having to save/reset every two minutes, so I've just given up), partly because remakes never have the same impact as the originals (they may be better - rarely - but they don't have the impact), and because there's loads of fiddly little extras in it that make me feel I'm missing out on half the game for not doing them all.
I don't like "one game for the price of two" things, but at least in the early gens the only downside to having just one of the versions was a few missing entries in the Pokédex (which otherwise would still be mostly full) - nowadays, not only is it nearly impossible to complete the Dex anyway thanks to all the trading and events required and so forth, there's all these other features I'm not interested in but feel I'm missing out on because they're there. I'd like to have a complete game when I buy it, and to be able to experience the entire game at my leisure. I could do that with the early gens.
Anything past the third gen (that includes all remakes) doesn't deserve consideration here. By now, the fanbase has way too make expectations for the series, and it'll never live up to them. The new games just won't be as good as people were hoping, and therefore won't have any impact other than "oh, I see Pokémon has a new generation out now". Way back after the first gen, when there were rumours of a sequel, we didn't know what to expect, which made it all the more fun to find out about gen 2. Nowadays everyone expects backwards compatibility, so Gen 5 will have it, which means it can't deviate too much from the basic format (battling and Pokémon-wise, at least), which means we know what to expect. And that's not as fun.