Gotta go with generation 4. It's the generation that I have the fondest memories of. It introduced online connectivity, and Sinnoh was a great region to explore. The music was pretty good for the most part too (the Team Galactic themes, Route 210, the legendary themes, and Champion Cynthia's theme come to mind), and while not the best evil team ever, I enjoyed Team Galactic quite a bit, especially in Platinum. Even some of the other characters were pretty enjoyable, such as Barry, Looker, Lucian, Roark, Bryon, and Cynthia. It even gave us the much needed physical/special split, and the Underground was an incredibly fun feature to use.
Perhaps what makes generation 4 my favorite out of all the Pokemon generations were the Pokemon introduced there. Almost the entire Sinnoh dex has my favorite Pokemon designs out of all the generations: you've got such amazing-looking such as Gallade, Lucario, Garchomp, Roserade, Dialga, Palkia, Giratina, Arceus, Darkrai, Weavile, Dusknoir, the starters, Staraptor, Luxray, Buizel, the Lake Guardians, Shaymin, Cherrim, Drapion, Magnezone, Froslass, Porygon-Z, the list goes on and on. Heck, a good number of them still remain my favorite Pokemon to this day.
Diamond and Pearl had some serious issues such as the slow battle and surfing speeds as well as unbalanced Pokedex that led to some Gym Leaders and Elite Four using Pokemon not of their type (I'm looking at you Volkner and Flint), but Platinum greatly improved those three issues, as well as bringing in more awesome features such as the Wifi Club and the return of the Battle Frontier; Platinum is also my favorite Pokemon game of the series.. I can imagine the potential Diamond and Pearl remakes will improve on gen 4 games even further.
Generation 3 is close behind as my second favorite generation, mainly due to the nostalgia of Ruby being my first Pokemon game as well as having another awesome caste of really well-designed Pokemon, a very memorable region, and some great characters. ORAS helped deepen my love for Hoenn even further with all the improvements it made.