Boy, where do I begin with the Explorers games?
First thing I can say is that it was really refreshing in my Middle/High-School years having a Pokemon game that felt like it took an effort the full way through, as opposed to generally being a coast and then having specific roadblocks or spikes like Whitney's Miltank or Fantina. It's easier to engage with the systems and the story when I have to be at attention throughout instead of turning my brain off and on again for boss fights or cutscenes.
I think one thing this sub-series does really well is taking advantage of the Pokemon themselves as a cast. Realistically speaking, I think Pokemon is more recognizable for the Mons themselves than the majority of human characters, with rare memetic exceptions like Gen 1 Gary or Anime Team Rocket. It also puts a neat spin on the same positions by assigning them to different NPC's between entries, like Chimeco as your Team Assembly in a sort of "nice lady/secretarial" air vs Rescue Team using Wigglytuff as almost a Barney-the-Dinosaur type of "friends!!!" framing to recruitment. In the majority of Pokemon games, mainline or spin-off, the Human cast can be good but still often feel like a necessary element when a lot of the stories still primarily rest on the Pokemon as heavy players like Ranger.
A common issue games like this can run into, as noted, would include item availability during dungeon stretches where you're cut off from the usual Town, but in Mystery Dungeon's case I can't say in my experience this has ever become a serious issue in practice. Even if not always the staple items, supplies are usually in sufficient if not excess supply compared to what I need for a pre-endgame dungeon, so as someone who usually goes into dungeons without a full inventory, I can build a backlog of supplies to replace my stuff with if I go down and lose things, at least long enough to re-establish myself. This on top of such sections of the game typically including Side Paths to each dungeon that are barely 3 floors long, so you can run them indefinitely without needing to invest any resources into the training until you're strong enough to make more headway on an incoming dungeon.
I also just find the games surprisingly replayable despite the linear nature. Besides the obvious elements like different starters or dungeon layouts, aspects can snowball into completely different runs even when sharing stuff, like different dungeon drops or money affecting your options to buy supplies from the shop, maybe Kecleon or a mission gives you access to a really cool TM either for yourself or a teammate you like to bring along, maybe you find some really neat lottery prize or get lucky with juice boosts at Spinda Cafe and the stats help you get over a hump without a ton of dungeon runs. Maybe you find some really good seeds that you want to save for one Boss fight as compared to another, or you just want to vary up the challenge like only using certain moves or not playing too many side missions. There are a lot of ways to tweak the experience of a PMD run that even with two identical starters the playthrough can vary heavily between different attempts.
And of course, I can't heap praise on this game without lauding the story. Something my friends like to reference half-jokingly is that this game is made by Spike-Chunsoft, who they mostly know for very emotionally swerving games like the Nonary games and Dangan-Ronpa. While not to the level I imagine those visual novels can reach, the Mystery Dungeon games are certainly willing to go to much heavier places than the main series games will on average (Sun and Moon are definitely outside the MG norm). Characters frequently commit to wrong or immoral actions that they have to answer for either in Karma (Team Skull get knocked around frequently for their wrong doing) or putting themselves through the ringer (Chatot is more trouble than help as 2nd at the Guild throughout the game, but throws himself against Kabutops and the Omastar brothers with no hesitation for others' sake). Even if the average character isn't a great deal more complex, they're put into much more strenuous situations with higher stakes (global or personal) that give a lot to discuss about what characteristics they do have: Chatot's Brine Cave scene recontextualizes his behavior from a by-the-book Rule Nut to a leader who wants the Apprentices to succeed, even if his strict nature may not always work as well as he hopes.
The story's big scenes also make their claim to the memorability of the game. Most famous is the ending's "Don't Ever Forget" scene, which not only avoids dancing around what is essentially death for the characters, but hammers in the weight of the scene by breaking from a trope of Pokemon (MD or otherwise): the player character distinctly speaks in dialogue for this scene. The concept that for the first and last time, an otherwise silent protagonist has to vocalize their thoughts not just for the partner, but for the player, without any "so you mean..." repeated lines, does a lot to set this moment apart from the rest of the story. Grovyle's return to the future is a similarly heavy emotional scene, dealing not with a character death as is usually downplayed in kids media, but evoking the same emotions and sense of loss by the forced and permanent separation all the same, right down to the contrasting dynamic of the player character knowing the truth while the naive/innocent partner at least thinks Grovyle will at least live to see the good future (even with Sky's Bonus Episode, there's no suggestion the Player or Partner ever learn the Future cast didn't vanish).
I could go on with the story based on some post-game plot lines like those pertaining to Darkrai and the fake dreams he gives the two, but this post has gotten long so I'll save that maybe for another reply or if asked.
