Sticker Star stripped down the battle system to a very basic form; stickers were required for literally every action including basic attacks, as opposed to how previous games used their special moves. Bosses are a sort of forced-puzzle boss; you can either insta-win with the right thing sticker, or do an incredibly long slog against them. And one of the biggest complaints is that it pretty much simplifies the story down to nothing - for example, Bowser doesn't even get any lines, there are no Paper Mario exclusive species, and other such things. Basically it would be a mediocre game if it was standalone, but the fact that it's a relative letdown compared to the previous Paper Marios is what makes it a bad game in the eyes of many.
The start is a bit slow but once it picks up it is a very solid game with some great humour. Most of the negative comments are just people having a cry about it being different to the first two games.
I loved the game, meself. It's good if you like plot and dialogue and can do without or would even prefer not having to go through lengthy turn-based battles, level grinding and difficult bosses to get to the cutscenes.
I never played too much of Super Paper Mario, but I did like what I played. It does start out a bit slow, I can agree on that, but it develops into a pretty fun game, in my opinion.
Though I never played the original two so I can't really give an opinion from that side.