I think @Gemsu, @Pantsman and @Gafle did a good job at explaining how to improve this anime, as this anime is clearly flawed, it's hard not to see it.
Now I will give my thoughts on how to improve SAO... Keep in mind I did enjoy both seasons, at least the first half of S1 and first and last part of 2.
I would get rid of the Alfheim Arc and extend the first arc, I don't know why they didn't do that. The build up would be much better for meeting the master, also there would be a much better leveling up sequence for Kirito, so he doesn't just randomly become the max level.
Then I would get rid of the harem, maybe like @Pantsman said and focus on a group and getting to know them. Have some politics thrown in, better guild system, spend more time on Kirito and Asuna so you can see their relationship grow properly.
Now with Kirito either than removing him, let's make him into a real MC. He doesn't have to be the ultimate fighter, make it so we see his fear (this is a fight or die situation), he is a gamer so I think he should've been more anti social especially when it comes to more serious situations, I think this years anime deconstructed the otaku character perfectly, and maybe make it so you actually feel pain in the video game world, if you think about it that does seem logical.
Asuna being a damsel in distress ruined her character, she was supposed to be a strong female character like from the start. So keep her like from the beginning and let her character grow.
Get rid of Calibur as well, it's just filler and a bad filler.