Pokemon R/B/Y are classics, but you will have to get used to doing some extra work in grinding than normal, and the battle mechanics look almost completely alien compared to how it is now.
Pokemon Gold/Silver is LOADS of fun. Vastly improves from the first set of games and even gives you a lot to aim for with Pokemon's post-game. This aspect is continued with Heartgold/Soulsilver on the DS.
Pokemon R/S/E are honestly pretty underrated, mainly because of some infamous long routes and the removal of the transfer feature, but otherwise its a great game. While it does have longer routes, it also feels a lot more expansive compared to previous titles, and it has tons of cool features like the secret bases and berry planting that give the game tons of variety. It's also one of the few Pokemon games where I actually felt challenged by the Gym Leaders.
I haven't played Diamond/Pearl/Plat, but I've heard somewhat underwhelming reviews of the game from the community.
Pokemon B/W is arguably the best Pokemon game yet. The loads of new Pokemon and unique environmental setting (being more urbanized compared to other regions) creates a very unique atmosphere that doesn't feel as "kiddy" as the others, and the whole game just proved that Game Freak is still capable of fresh ideas. Even smaller details, such as how the villainous team and the region professor were integrated more into the plotline, really added to the experience. I say it's only downside were that the Gym Leaders were so easy they were almost forgettable.
I haven't played B2/W2, but I've heard there is a lot you can do in those games.
Pokemon X/Y honestly isn't worth it. While it did many things to make the competitive angle of the series more approachable and less of a chore to get prepared for, it fell flat in just about everything else. The 3D graphics are nice, but unlike other 3DS games it doesn't utilize the 3D features to its fullest extent. The camera positions could also get out of whack in some areas, zooming too closely to your character (which obscures vision needlessly) and even creating navigational problems like in Luminose City (GOD I hate that place). The game also had a lot of ideas that, while good on paper, were terribly executed. The Pokemon ride sections came with slow movement and clunky controls, the Horde battles are a NIGHTMARE and yield low rewards for the risk of engaging them, and Sky battles require that you go out of your way to build a specific team in order to have a fair chance in battle, yet they don't reward you anything different from what you'd get from normal trainers. That's only naming a few. The fresh feeling of B/W is also somewhat removed from this game. For example, instead of a lot of new Pokemon, they only have about 70 or so, and the rest of the HUGE national dex (around 400+) is crowded with old Pokemon; this is made worse by the fact that so many Pokemon with similar roles (Like Bidoof and Sentret being in the SAME ROUTE) were jammed into these routes, making this feel like some kid's fangame where every species is thrown about randomly rather than a fresh, competently designed experience. By the way, did you like having the expansive post-game of G/S or B2/W2? You'll be disappointed to know that all there is to do after beating the game is go on an arduous hunt for Mega Stones and play the broken Battle Frontier. I can't call it a bad game, but it's definitely one of the weaker entries to the series, and it whole game felt absolutely dull.