I haven't played Gates to Infinity, nor will I ever play it anytime soon. I've heard nothing but bad things about that game.
PMD2 (Explorers of Darkness/Time/Sky) is the best in the series. I played the originals too, and while they are fantastic, they can't beat Explorers. It's just that good. Story, gameplay, music... almost everything about is fantastic. If you cried while playing the originals then you'll cry twice as much in Explorers. Explorers is a bit darker than the originals.
PMD is one of my favorite video game series ever. In my honest opinion, they are better than the mainstream Pokemon games. R/B Rescue Team is fantastic, and Explorers of T/D/S is even more so. Charming graphics, good characters, fun gameplay, amazing music... the games are so good. (haven't played Gates to Infinity but I heard that game is bad).
I've been playing PSMD for the past 2 and a half hours and I've been smiling ever since. Everything about it screams PMD. The graphics, characters, story, music, and dialogue all combine to make a fun and cute as hell game. I'd totally recommend it.
I want to emphasize on the story and music of this series. PMD games are tearjerking as heck. Explorers of Darkness is one of the very first games to make me cry. The originals were pretty damn sad too. The music is perfect. Epic, sad, cute, funny... it fits the scenes so well.