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Rescue Team: The first in the series, had a lot of questionable design choices like "the team members dispersed to friend areas" limited recruits per trip, and a load of 99f dungeons. Groundwork was laid here, still a fun game. You could give everything Super Mobile easy.
Explorers: Obvious upgrade from the first game. More item space in the bag, longer story, no pokemon exclusive to level 1 dungeons. Randomized missions give far better rewards than in Rescue Team. Special Episodes to give certain characters more story. Main questionable section here is everything about Aegis Cave.
Adventure Squad: Most people forget this one exists. Entirely in Japanese, split into three, and has some weird mechanics not seen in the rest of the series. Language barrier will keep most people from playing.
Gates: Fewest pokemon of any of the games. Hellishly slow text speed, 1 mission at a time, and no online rescues. Notable positives include the characters, Paradise, and Team Skills. Overall feels like it was rushed to just have a pokemon game on the 3ds.
Super: All the pokemon are in here, outside of Volcanion. IQ skills are gone and replaced with Emeras, the normal attack's power is gone, randomized missions are gone, and so are region free rescues. Easiest game to 100%, due to all pokemon joining eventually. Thought of to be the hardest PMD, backed up by a sudden difficulty spike early on, and is the only PMD with multiple towns, which is nice, if done a bit poorly. The biggest flaw here is the break system, which never fully goes away. Overall feels like the game was rushed to release before the Sun/Moon announcement. Not a bad game by any means, but leaves some people wanting more.