This is a quite good topic but not the easiest to answer. I'm sometimes not sure what counts as unpopular since it is hard to know if the majority of the fandom agrees with me or not regarding many things. I find myself to agree with a lot of things others have already posted here, even if most of these things probably are unpopular regarding the fandom in general. But anyway, here are some of my own.
HG/SS are among my least favorite games in the series. In terms of the enjoyment I have gotten out of all games in the series that I have played, they are at the very bottom. The main thing that ruined them for me was the horrible level curve and the lack of good training spots, and the rest of the things they had to offer did nothing to make up for this. I felt like the games were filled with wasted potential and opportunities that they never made something good with. I didn't like how features from previous games were either removed or copy-pasted, and I didn't care much for any of the new features. I strongly disliked one feature in particular, which is my next point for the thread. These games were also released when my interest in Pokemon was at its all-time low, and they did nothing to make me regain my previously higher interest in the franchise. There wasn't a lot of things I liked from these games, and if it hadn't been for those very few things, I couldn't have asked for worse remakes.
I don't like the following Pokemon feature, at least not the way it was done in HG/SS. I could tolerate it in Yellow and D/P/P, but that's because I felt that it was much better done there. In HG/SS, there was nothing I liked about it. The feature didn't feel like it was well implemented, the Pokemon were stuck in a two-sprite cycle instead of standing still while the player stood still, and walking as the player walked, like it was in Yellow and D/P/P. I had expected to be able to choose which Pokemon to follow me, but no, it was always the first one in my party. Always. Which is another thing I didn't like about the feature, you were forced to use it throughout the whole game. Was it really that hard to add a function to just turn it off? If this feature returns in any future games and if it works the same way as in HG/SS, I won't get those games. I'm dead serious.
The idea of future Kanto remakes or re-remakes disgust me. I got an urge to vomit the first few times I heard of this idea but have since then grown a bit more tolerant of it even if I still strongly disagree with it. I do personally never want to see Kanto in another game, having seen it in four generations of which I only really think one did the region well, I would be fine if we never got to return to it. I have always hoped that Game Freak would focus on creating new games instead of trying to recreate the past, but given recent developments for the franchise and the company, I fear the worst. In case those games should happen, it is very unlikely I'll get them even if they would turn out to be good.
On the topic of Kanto remakes... I think that FR/LG are among the most underrated games in the series. While they are not my personal favorites, I like them and I think they are much better remakes than HG/SS were (haven't played OR/AS so no opinion there). When I look at polls for the best games at Pokemon sites, FR/LG usually has either zero votes or just very few, and people in general seem to either dislike them or like them but not have them as their personal favorite, which is a category I fall in too. All the people who ask for Kanto remakes need to remember that two excellent ones already exist, albeit slightly outdated by modern standards.
I like almost all Pokemon to some degree. There are only two I can say that I actually dislike and that is mostly for personal reasons rather than only because of their designs. It has never made sense to me how people can be fans of the series but actually dislike a large chunk of the creatures that make up the very core of the franchise. Naturally, some Pokemon seem a bit weird for me when a generation is new and when I first see them, but they grow on me over time. For example, I thought Chesnaught and Barbaracle were weird when X/Y were new, but both of them have grown on me with time.
I try to find inspiration in every single design. Sure, I have gut reactions with certain Pokémon, but most of the time said reactions aren't negative. There are only a handful of designs that I don't like, and for probably the majority of them, the reason is just that they are uninspired.
I pretty much agree with this.
Dunno if this is unpopular or not but it's an opinion I don't really see often. HG/SS are objectively the best games in the series. and they're as close to perfection as you can get in video games. I know I'm exaggerating here a bit but I really believe that.
First of all, this is not an unpopular opinion in the slightest, I can promise you that many people will agree with you (as in HG/SS are their favorites or among their favorites).
I disagree though. To me, they are among worst in the series and I think they are highly flawed and imperfect games (explained parts of why I think so earlier in this post, willing to go into more detail if people want that). But beyond that, they are not "objectively" the best in any way because such a thing does not exist, what games we find good or bad are subjective, nothing else. You are welcome to think HG/SS are the best games in the series, that's your opinion and that's fine, you are entitled to it. It makes them the best in your personal subjective opinion, if anything. But saying they are the objectively best, especially without backing it up, and posting a popular opinion like that in a thread about unpopular opinions is not a good thing, and I'm not sorry for saying that your post is one of the worst ones I have ever read.
That's all I had for now. I might have some more unpopular opinions that I can't think of right now, and some that I'm not sure whether they are unpopular or not.