Yes, even your favorite Gen has some type of controversy surrounding it and is not as well liked as you might think.

Gen 1:
>It's a buggy mess
>Incredibly simplified
>Boring ass plot
>The fact that it exists at all nowadays.

Fans who came into the series later don't give a fuck. Most newer fans rightfully see Gen 1 as bland and overhyped, with most of its love coming from the people who grew up with it during the Pokemon hype craze of the late 90's, and are much more reluctant to highlight its flaws.

Gen 2:
>Is basically Gen 1.5 in practice.
>Non-linearity

Tell that to the people who had to grind about 4-5 more levels after Clair because you were still in the mid thirties, with all of the trainers being at that level as well. The level curve was always considered a problem, which carries over into Kanto as, not counting the remakes, all of their levels are far lower to pose any challenge. It was great for it's time because it had never been done before, but as I said, newer fans don't have that context. So it comes off as ultimately superfluous.

Gen 3:
>Too Much Water
>Plot is stupid
>Not all of the Pokemon were available from the start and were sold later (sound familiar)
>Pokemon Contests
> No Battle frontier in ORAS.

This is essentially when things really got controversial; yes, they did the National Dex thing before, crazy I know. But nobody cares about that for some reason :V This is also people nitpicked about "unnecessary gimmicks" such as Contests, and the plots being stupid.