The people saying the MC is a Mary Sue are not exactly right but not wrong also.
The MC, before getting poisoned, is described as being "perfect" in everything she does, being stronger than everyone, having a body that is superior to all others and is loved by everyone "good" while having all villains envy her, those are the characteristics of a Mary Sue.
That makes the claim to be "right" but since she did succumbed to the poison getting out of the loop for 20 years and reclaimed her memories we don't have enough time to know if she will keep being "perfect" and even if so it is not automatically a bad thing as with good writting even a Mary Sue can be entertaining to follow, I mean people do like SAO and Kirito is clearly a Mary Sue and the writting is not that good.