Not Bait disclaimer. I firmly believe that Gen 5 started Pokemon's downward trend, and was the biggest stray away from the series' roots. This is not to say that Gen 5 was bad, on the contrary, it has a lot of great aspects. However, it carries with it some issues that would compound in later releases.

The biggest issue people bring up is with the new dex. Designs can be subjective so I won't dwell on this too much. The aspect I will dwell on is the repetition. In Gen 5, we were given the largest new batch of Pokemon to date, a whole new dex capable of standing on its own. And in many ways, it did this very well. Its main issue is redundancy and feeling the need to repeat older trends despite having the pitch of a new dex, a new experience. For example, the Conkeldurr line is effectively just Machamp, but with min-maxed stats. Roggenrola's line is just Geodude but without the Ground typing (which is better than the previous example). Pokemon as its dex has grown larger has struggled with this issue of redundant Pokemon bloat, and Gen 5 exasperated this issue needlessly, seemingly feeling that people love rehashes of concepts like the early dark type, the normal/flying bird, or things like the monkeys.

The second-largest issue with Unova is how it felt the need to be a pseudo-reboot in terms of features. Where previous generations tried to build upon older features, Gen 5 largely scrapped a ton of them with no replacements, or gimmicky ones. Pokeseals, secret bases, pokemon by the time of day, contests, all gone. Instead, we got the musicals, a gimmicky one gen thing, dream world, a gimmicky now-defunct one gen thing, and seasons, a gimmicky one gen thing. This is one of modern Pokemon's biggest problems, and it comes back to Gen 5.