What I've always felt about the Pokémon Mystery Dungeon series, is how amazing it's storyline is made and how different it is from most other Pokémon games. Spike Chunsoft certainly has made some extraordinary Pokémon Mystery Dungeon games. As new hardware is made, new graphics and objects are made to take full advantage of the new hardware that it's made for.
Storywise, I liked all of them. But if I had to pick, it would be a tie between Super Mystery Dungeon and Explorers of Time/Darkness/Sky. Gates to Infinity was also amazing in how it was able to handle the cutscenes and the animations of the Pokémon (.bcmdl) models, so too was Super Mystery Dungeon.
As for gameplay mechanics, Explorers of Sky had the best out of all of them. The Adventure Squad games on WiiWare did lack some things that Explorers of Sky had, but was the first 3D Pokémon Mystery Dungeon game. Sadly it didn't get released outside of Japan due to the GFC that occurred in 2009-2010, resulting in poorly selling games to never be localised into other languages. As for Gates to Infinity, it lacked many of the gameplay mechanics that previous PMD games had, and no longer had a breeding mechanic or different genders for Pokémon, also only had a handful of Pokémon, mostly Unova Pokémon, and a few from other regions, but had a new dungeon mechanic called gridless floors, which allowed Pokémon to move around freely until they moved into an enemy Pokémon and would start a battle. Super Mystery Dungeon did bring back a few functions, but removed the gridless floors from Gates to Infinity, but did include all the Pokémon except for Volcanion.
As for sales, from what I can see, Explorers of Time/Darkness sold very well. But Explorers of Sky, despite being a more improved game, sold poorly, probably because of three things:
1. Same storyline as Explorers of Time/Darkness
2. From what I've heard, Explorers of Sky didn't manufacture many copies anywhere.
3. The GFC may have contributed to it's downfall in sales, which also leads to #2 which is stated above.
Will we get another Pokémon Mystery Dungeon game? Why yes, it's possible! But to get better sales, it will need to include all mechanics from previous PMD games, including gridless floors and gendered Pokémon (along with the breeding mechanic). But it will need significant new mechanics into the game too (eg. Hub overworlds in which can be explored in a gridless floor-like function from Gates to Infinity). It will also need functions that allow players to interact locally and over the internet, to give it a good purpose to even be enjoyed by anyone. It will also need to be localised into Korean and Simplified Chinese and Traditional Chinese, and South Korea has never had a PMD game after Explorers of Time/Darkness.
To me, I've always loved the 3D PMD games, mostly because of the capability in what it can really do to achieve great cutscenes that are not possible in a 2D PMD game. Judging from what Spike Chunsoft has been developing lately, the last Mystery Dungeon game they made was actually made for Windows and it was in 2D. Wouldn't it be nice if they could also return to the Shiren the Wander series again and make a 3D Shiren the Wanderer game? After all, localisations of earlier of those games are being made and ported to platforms such as the PSVita. But Spike Chunsoft is not in charge of the Pokémon Mystery Dungeon games, The Pokémon Company is though. So it will be up to The Pokémon Company's President to collaborate with Spike Chunsoft to work on making another PMD game.
For the next Pokémon Mystery Dungeon game, please make it become a real adventuring game with it's dungeon crawling mechanics and also have actual humans appearing in the game as well, not just Pokémon. And please keep it in 3D.