Platinum is not only my favorite game of Gen 4, but also the best in my opinion. Solid plot, excellent challenge, decent variety of Pokemon (still very few Fire-types, but no game is perfect) and a lot of fun.
Also Team Galactic. Until Ghetsis, Cyrus was by far the most interesting and insane Big Bad. He may not be as...appealing as N, or as charismatic as Giovanni, but he had the biggest ambitions and the biggest story. Anyone who comes that close to wiping out the universe deserves to be called one of the best villains in the series.