Blue Rescue Team, because friend areas. Chimecho Assembley and the Connection Orb were both lazy and uninspired, and that lack of a personal touch didn't give the later titles much in the way of charm, really. Even though it has the fewest Pokemon in it, at least I got to see them absently wandering around in their free time. In a series like Pokemon, where very little changes, the little things count, and taking out friend areas was the biggest mistake they made with the series.
Super Mystery Dungeon gets points for including every Pokemon and making them actually recruitable, though. The recruitment rates in the DS titles were obscene for some Pokemon, and no Arceus in Sky outside of a pointless statue was...vexing. Although SMD pushed you through the story at an uncomfortable pace that I didn't care for.
...obviously I won't be talking about Gates to Infinity. That doesn't qualify.