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I'm new to the Mystery Dungeon games, so I'll just share my experience so far and hope it helps.
I wasn't really interested in giving it a chance for the longest time, but when Gates to Infinity came out, I had some extra cash and thought "why the fuck not". Bought it, played it, and loved it. I could see its flaws, some of them glaring, but they didn't keep me from having fun.
After beating it, I looked around for opinions on the best Mystery Dungeon game, which led me to buying Explorers of Sky. I'm playing through that now, and in every aspect of gameplay, Explorers of Sky actually feels like a sequel to me. It's like it improved on the design, despite being the older game. I can see why people who followed the series were disappointed with Gates.
My cousin has a copy of Blue Rescue Team that I plan to borrow and see what that's like after I finish Explorers. Funny how I'm working through the series in reverse order like this.
So, from my limited experience, and considering you don't have a 3DS, Explorers of Sky is the only recommendation I can make. Hope this helped.
