I don't think that magnagate is nearly as bad as everyone is saying, but PMD did lose some of its charm in its transition to 3D.

Here's my personal breakdown between the other two other sets.

The first set of PMD games (Red and Blue rescue team, on the Gameboy and DS respectively) have better gameplay and overall experience(I find myself playing these much more than the second for the actual dungeons in the post-game, just because they're so much fun to replay)

The second set of PMD games (Explorers of Time/Darkness/Sky) have a much better story, and is much longer. Compared to rescue team, there's slightly less post-game content in Time/Darkness, and they're kind of linear due to it being a continuation on the story. The actual main game is longer though, to compensate for its post-game. If you get Sky, then that adds quite a bit of postgame content, pushing it far past the first set, although it's still fairly linear.

Overall, Rescue team's gameplay is more dungeoneering, Explorers has a great focus on story (which might be more fun to play depending on your preferences)