he thing is Game Freak has been around longer than Pokémon (not a huge company, but still), and they made a few other games even during the Pokémon era (mainly Drill Dozer and Harmoknight, and I believe those games are decent?)
I'm surprised they haven't done sequels to Harmoknight and Tembo the Badass Elephant. Those are games that were positively received by critics, yet they haven't been heard of since. Maybe that's a sign that GF's staff is too small to handle multiple games, or there is not enough time between developing the Pokemon games and other games.
While there's really no source I can find confirming this, it's at least widely believed the relation between GameFreak and Nintendo is a strained one. Both probably see each other hard to work with, Nintendo being more corporate while GF being more casual. I can see the GF execs dreading having to meet with the Nintendo execs because they know they're going to have to come up with deadlines when all they want to do is make GAAAAAMEs. Meanwhile Nintendo execs massage the bridge of their nose hoping the thoughts of just strangling the GF execs and taking the Pokemon franchise via bloody conquest doesn't cross their mind as they try to extract the vaguest of timelines like a dentist does with cavities.
I'm not sure if Nintendo is the source of the rushed Pokemon games. If anything, they are allowing more development time for their main IPs to ensure that their employees aren't overworked, which is common criticism of video game companies like Konami and EA. Examples include Fire Emblem: Three Houses and Animal Crossing: New Horizons, both of which were delayed to ensure the highest quality as well as to make sure their employees are not overworked. That extra time is incredibly important in Japan, where the work is so important to the point that you are expected to be dedicated to your work 100% all the time on the weekdays with no time for extracurricular.
Hopefully I'm not bleeding too much into "unpopular opinions" (though I suppose the threads are kind of similar anyways) but I honestly think the Pokemon games aren't remotely living up to their potential and I mean that from a commercial prospective. Pokemon Go racked up over a billion installs before most people dropped it (which I think is due more to the game being bad than people just checking out the trend, though certainly the latter is a big factor as well) and the sales of the game are pretty bad in comparison. Obviously a free-to-play game will have more players by virtue of being free but I can't see any reason why a relatively niche game like The Witcher 3 should sell nearly twice as many copies as Sun and Moon. I've talked to tons of people who have fond memories of playing one of the first 4 Pokemon games as a kid but who fell off the franchise afterwards and every time they seem kind of interested when a new game is announced... and then seem way less interested when they see it's basically the same game as before. It's not really surprising considering that the game has very little in common with any of the popular trends in modern gaming. E-sports are popular? Gamefreak has a great competitive system...buried under stupid shit like IVs, rarely acknowledged by the actual game and not even present in Pokemon Go. They did at least pivot to the Open World formula but it looks like a pretty half-assed attempt at it (I haven't played the last two games) and I wouldn't be surprised if it was just absent from the next game. Some difficulty settings could also go a long ways to bringing back older fans who fell off at some point. I could go on and on but seriously the third installment in the dark fantasy Polish folklore game shouldn't be outselling Pokemon. 16 million is a huge number but it's also about half of the first game and about the same number they've been pushing for nearly twenty years despite a much bigger gaming market these days. Another reason why I don't buy the evil TPC theory, Sword and Shield were pretty clearly held back by Gamefreak's lack of desire to expand their staff and as I hope I've highlighted I don't even mean that in an artistic sense.
Well to be fair, SwSh added Nature Mints and Exp. Candy which have definitely lowered the bar for competitive battling significantly alongside TRs and redone egg moves and mechanics.
I dunno if this counts as unpopular or not, but I really think Pokemon Go handles the Pokemon themselves significantly better than the core games. For starters, you can't just mash buttons or breed to get the Pokemon you want, you have to actually walk and travel to new places to encounter new Pokemon, which requires an amount of effort. More reasons why Go expresses Pokemon better have been stated, but a personal example was when I got a Volbeat, a region-exclusive Pokemon during this Special week. When I was the last time I got excited over a Volbeat?
I even like how battles are handled. While there are some undeniably better Pokemon than others, unlike the core RPGS, you can't just go on forums or go in game to get a Pokemon instantly. Instead, you have to actually physically find the Pokemon, which can take a huge amount of effort since you have to walk.
Let's look at Alolan Ninetales. Its considered a strong pick for Great League battles, but since you can only hatch an Alolan Vulpix from eggs that came from friends, you are going to have to dedicate some time hatching eggs that you only have a chance from friends. And if you even have to hatch that Alolan Vulpix from the egg, you also have to dedicate some time to get candy in order to evolve it.
While you could wait for that Ninetales, you have to wait for the possibility that you will miss rewards if you try to grind for the Ninetales, So the better solution would be to use Pokemon already you have in the party, Like Glaceon, Walrein, or Alolan Sandslash and try to attempt the Great League. The fact that you can't just get an optimal Pokemon within minutes forces you to use Pokemon that you already have, which might be good or bad, but it does allow bad Pokemon to receive spotlight even if they are outclassed. Even trading has limits to ensure that People can't trade to obtain powerful Pokemon through stardust and friend cap.
A little late on this, but also there are no Pokémon Amiibo apart from Smash characters, and crossovers with Pokémon into other Nintendo games is pretty non-existent too. TPC is
really protective of their IP, and reluctant to participate in anything involving sharing of their creatures or designs.
Also,
JourneybyTrain, the reason why Pokémon Go has such a strange battle system is apparently because Niantic weren't allowed to use the mechanics of the core series games. Apparently, they didn't want direct competition between the games, so the battle system in Go boiled down to rapid screen tapping while Pokémon weren't trained, but fed. Some changes have been made in recent updates, but it's still a very far cry from the intricate system that granted the main series such success.
The biggest and strangest omission would be the Yoshi's Wolly World Series. These series allowed you to scan Amiibos to unlock patterns for Yoshi based off Amiibos you scan. As of the 3DS release, the games pretty much had every Amiibo compatible, regardless of how rare of it. This includes: Mario, Zelda, Metroid, Kirby, Kid Icarus, Fire Emblem, Splatoon, and even third party Amiibos including Mega Man, Sonic, and Street Fighter.
Yet, NONE of the Pokemon Amiibo grants Yoshi a pattern. Yes, they have skins for Mega Man and Street Fighter, but Pokemon. The developers said that they couldn't come up with any "Sataisfying" design for Yoshi, hence no Pokemon designs. But considering every Amiibo except Cloud and Bayonetta and Cloud had Amiibo patterns, the real reason was probably because TPC did not want to license the design to the company.