Not "unpopular" but definitely an extremely divisive opinion; I really like Gen 5. I completely understand why it wasn't to everyone's taste, I found the overall aesthetic hit-and-miss, but I really love a lot of the Pokémon designs, the music is for the most part Really Great, it gave us a lot of awesome bug types - but I find myself replaying Black and Black2 a lot more often than any other games bar Gen 2 and HGSS, which are my favourite games overall. The difficulty curve is one of the best in any Pokémon game (not saying it's great... but it's something), and the heavy inclusion of Gym Leaders in the plot was really fun. The plot is a little hamfisted, but it was a solid attempt.
Unpopular: I grew up with Gen 1, my first game was Red shortly after it came out here in the UK, but... Gen 1 is so lackluster for me, and always has been. Whilst I have a lot of great memories from playing Gen 1 as a kid, I find it an absolute slog to replay, and as a kid I enjoyed it only because it was a Pokémon game, not because it was a good game. Once GS came out, I pretty much only touched RBY when I needed to trade up exclusive Pokémon for my PokéDex. Though I have replayed it many times since the Virtual Console versions came out, it's not my least favourite Gen but it's just so... meh.
Unpopular 2: I see people get upset about the abundance of cat and dog-based Pokémon but I don't see a problem as long as it's only 1 cat line and 1 dog line per Gen. Cats and Dogs are some of the most popular pets the entire world over, so it makes sense - and thinking about all the different real-world dog and cat breeds out there in the world - I think it's pretty fine.
Unpopular (?) 3: We need more bug types.
Unpopular (?) 4: We need more pigeon Pokémon. Like point 2, pigeons are extremely abundant the world over. Most people don't seem to know this, but there are hundreds of different wild and cultivated species and breeds of pigeons - I was ecstatic when we got Pidove but the fact it evolved into a pheasant was kinda dumb. Maybe it's because I really like pigeons so they're Serious Business to me or something. (For those interested in different types of pigeons, I recommend looking up these fancy/domestic breeds: Capuchin, Fantail, Lahore, Chinese Owl Pigeon, to see the diversity which has been bred just from the Rock Dove/"street pigeon", and for wild ones, Japanese Green Pigeon, Victoria Crown Pigeon, and Crested Pigeon show just a tiny snippet of the different types there are out there).
I say that one as unpopular because whenever I've mentioned to people "more Pigeon Pokémon would make sense/be cool", the idea always gets shot down, so I guess it counts?