I've never played GTI or Super, so idk how much water this opinion holds, but as much as I like Mystery Dungeon, there's something about the series that bothers me a lot:
The Mystery Dungeon games do away with one of the core Pokémon series's main aspects: using different Pokémon. The fact that you're forced to use your starter and partner through most of the campaign can make the actual main story of Mystery Dungeon a bit less fun to play through than it usually would be, and sometimes downright cruel, especially when, let's say, you pick a Treecko in Rescue Team and get stuck on Mt. Blaze. The Explorers games take this problem even further because of just how many dungeons you're forced into using only your starter and partner. The fact that you can't evolve either is obviously a necessary concession for story purposes, but I'd rather that not be the case, because forcing the starter and partner to never evolve doesn't give the game a good sense of progression.
I'd honestly really like if Mystery Dungeon took cues from something like Etrian Odyssey, where you're allowed to play with team composition as much as you'd like outside of sidequests and missions, while the main story progresses. (Once again, I've never played GTI or Super, so if this is the case in either or both of those games, lemme know.)
On an unrelated note, I have some mixed opinions on Rescue Team DX as a remake.
One one hand, I really like how it ironed out many of the original game's problems, especially when it comes to recruiting Pokémon. In fact, recruiting Pokémon is actually a really fun time, because who doesn't like leading a caravan of up to eight Pokémon? I like that they added a risk-reward factor to it as well: newly recruited Pokémon have unlimited PP, but there isn't always safety in numbers, as if any member of your team faints to an enemy, that enemy becomes stronger. The remastered soundtrack is also a joy, because it strikes a balance between "faithful recreations" and "worthy remasters."
On the other, I don't like that they added absolutely nothing to the main story, and it's still as short as it used to be. I don't like that they changed dungeons like Western Cave either, because I honestly liked the original, longer version with powerful Pokémon, and I don't like that Murky Cave is now a clone of Waterfall Pond. They've made some strange decisions too, like for some reason removing Nincada from Lapis Cave and forcing you to go to Miracle Sea to recruit one? What's up with that? Joyous Tower is also obsolete, now that the Pokémon you'd normally only find there can just be recruited in random places. I really don't like how slow it is compared to the old PMD games, either, which makes already long dungeons a slog because of animations and downtimes taking longer than they need to.
I'm not sure my opinions on RTDX are exactly unpopular, but overall I think they're good remakes with a few questionable design decisions.