Sword Art Online's Alicization arc was actually pretty good. The plotline is solid, Eugeo gets actual character development, Kirito loses a fight, and Kawahara found out how to make sexual assault look like a bad thing (only took 3 fucking seasons). The fights are now less about "who's better at stabbing other people" and actually utilize the environment around them for once. Eugeo vs. Bercouli stands as my favourite fight in the whole series.
Since you can never talk about SAO without bringing up it's problems, I am going to say that Fanatio's story kind of doesn't make sense. She claims to have hidden her face because she didn't want her opponents to handicap themselves, but it's pretty clearly shown that most people, including the integrity knights, don't really care about the gender of their opponent. I also kind of don't like the final fight of the series, as a lot of what happens seems really asspull-y and the deaths seem incredibly forced.
The war arc is also really good. In a vacuum, it's pretty good, and it's definitely the best arc in SAO. Kirito is almost completely taken out of the picture for most of the fight, and the show is overwhelmingly better off because of it. Fights have much more on the line because the main character can't bail out the good guy if they start losing, and he's not there to beat the hell out of everyone remotely dangerous to the rest of the main cast. The old cast members are brought back, the emotional moments are actually emotional, and the new characters introduced have a personality. The plotline is good, there are actual stakes on the line this time, and the final villain fight is not exactly terrible. Was the last fight a bit of an asspull? Yes, definitely. Do I care? No. The animation was cool as fuck, and it's the only time I've actually rooted for Kirito to win through the show's 80+ episode runtime. I'd compare the villain fight to SAO 2's final fight, but instead of being the only good part of an otherwise terrible arc, it's an iffy ending to an otherwise fantastic arc. Then, the ending scene was so utterly nonsensical that it forced everyone to keep the show in the back of their mind to find out why kirito "fought" a big ass space squid for literally no reason.
I am not counting the GGO spinoff as the best as it wasn't written by Kawahara and therefore should not be compared to any part of mainline SAO.