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I only played Pokemon Super Mystery Dungeon and really enjoyed it. The plot was great and good surprise after the "slow" beginning. I didn't really mind the beginning plot like most people seem to on here. I put in 122 hours and got every pokemon, all treasures and visited every dungeon.
Gates has nice story and characters for PMD, and a neat side attraction with base building, but is blatantly lacking in gameplay with a tiny Pokemon roster and some simplified mechanics that go beyond streamlining into straight up dumbed down
Super has great dungeon crawling, but the general structure of the game is neutered with the new recruitment and mission systems, and the story is some of the worst s*** I've ever seen in a video game
Etrian Mystery Dungeon is buggy and poorly designed but I hear the currently unlocalized EMD2 fixes everything and makes the concept work
so I guess Super because the core dungeon crawling is actually great but everything else about the game is excruciating, if you like PMD for the story play Gates instead