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I've never played Gates to Infinity yet, and the only other Mystery Dungeon games that I've played were Blue Rescue Team & Explorers of Sky, so I'd go with Explorers of Sky.
Soundtrack's fantastic in my opinion, the plot was alright, though I will admit it was a bit Mary Sue at times, but that didn't prevent me from enjoying it. The ending made me cry like a bitch, I will admit, mostly because I felt incredibly bad for your partner.