I am slow at beating games. I usually don't get a ton of time on weekdays, when I have other things I want to do too. But I just got the adorable scarves.
I have played all of the Mystery Dungeon games to date, beating main and post stories. I love the series as a whole, especially for the story elements. I'm thinking of restarting Super and doing another playthrough.
Explorers of sky is still my all-time favorite. The storyline and the events affecting the main character seem to flow the best and make the most sense. Gates to Infinity is my least liked . It has the least amount of content, too much DLC that it feels like a cash grab, and a post-game that is barely existent. Super is certainly enjoyable, but it does pull a stupid move in the form of the main story final boss. Pretty much copying what Gates did. Seriously, I liked it better when the villain was a Pokemon that had a reason for wanting to commit the atrocities they did, not some shapeless entity of emotions and crap.
Blue/Red was fun and about average for me on the scale.
Overall: Explorers>Super>Rescue>Gates
Team Alpha
Rescue: Torchic/Eevee
Explorers: Riolu/Vulpix
Gates: Oshawott/Snivy
Super: Riolu/Fennekin (Next playthrough, Chespin/Fennekin)
Yeah, the final boss of the last two games were... odd. I thought it was interesting, but odd. Also, during the last two final bosses I noticed you don't restart them when you get defeated, but everytime you get back into the battle you keep going where you left off. In Super I managed to do it in one try (with luck, strategy and a bunch of reviver seeds), but it had so much HP. It felt ridiculous, it took so long to take the core down.