When I first sat down and watched SAO, all that I heard about it was it's reputation for the incest plotline, people praising it and claiming that it was "Anime of the Year" material...and it's apparent popular following when I attended Anime LA '13. That said, at that point I didn't really follow all the hype and news in the online anime community, and when I watched SAO, it was long after the show had finished airing.
And when I sat down and watched it....I was incredibly surprised and disappointed in what I found.
I should note that I think BOTH story arcs are bad in their ways. Sorry people, but I don't care how entertaining it is; some of these flaws I can't ignore, and they pile up enough that they can't be ignored.
-Kirito is a Gary Stu
-Romance between Kirito and Asuna is under-developed and a little bit unbelievable
-Side characters coming and going with no carryover (which from what I understand, it gets worse as the story progresses)
Aincrad arc problems:
-Pacing feels incredibly rushed
-Our "antagonist's" motivation is so vague, that even he doesn't remember it
Fairy Dance arc problems:
-Antagonist is so completely over-the-top, creepy, and moustache-twirling evil that it's almost funny
-Incest plotline (although personally I don't think it's quite as bad as how people paint it)
Personal debatable problems:
-Inappropriate placements of fanservice
-The show undermining it's own themes
And of COURSE there are going to be people that are going to bash on things just 'cause it's cool to bash on it. There always is. That said, legitimate criticisms can't be ignored and shuffled off as "haters gonna hate". I was for the most part unexposed to the hype, and I still didn't like it.