Gen 3- Ruby and sapphire had a partial pokedex like sword and shield. 7.5 out of 10 too much water. This is most likely a problem people see looking back but If you wanted a complete national dex back then with no help you needed 2 GBA's, a NGC, GBA link cable, GBA to NGC transfer cable, and the games Ruby, Sapphire, Fire Red, Leaf Green, Coliseum, and Gale of Darkness.
Gen 4- the overall speed of the game is the main complaint.
Gen 5- you could only use pokemon from Gen 5 until the post-game.
Gen 6- lack of story, mega evolution makes it too easy, Team Flare, Lack of postgame content
Gen 7- too many cutscenes, Z-moves make things too easy
And to top it all off people during each gen will complain about lack of a jerk Rival and that "This Generation has the worst designed pokemon ever" particularly around gen 4 & 5 for most people.
Basically there is always conplaints about pokemon yet people still keep coming back. And this is all just what i remember off the top of my head