The "Asuna loses all competence and becomes a maiden in a tower" thing that I remembered fairly strongly really seemed to not be present near as much as I thought it was. Looking at it now I can only think of once or twice where it slipped close to the "competent character is kept locked up because she is a woman" instead of "competent character, who just happens to be a woman, is kept locked up". I mean not only does she successfully escape her cage, but after her attempt to hit the logout button is foiled she tries
again with her foot, and even when that fails she still manages to grab the entrance key and hand it off, ultimately allowing her own rescue. That's certainly more than Frodo managed to accomplish when he was captured by the Orcs!
And as for the "fake sister"/cousin love angle, it was definitely still present, but I found it rather tolerable this time around due to a couple of things:
1) It's definitely one-sided. When Kirito actually hears about it, the one time we get to see him react it's given almost word for word the "I just don't know what to think about this", rejection-esque response, and even in the little tease in the epilogue and whatnot I didn't pick up anything more than platonic from his side.
2) Suguha tears herself up about it and tries to deny it. She goes so far that, in fact, had it not turned out that her "replacement" she was looking at happened to be Kirito as well, it probably would never have come to the light. She was totally committed to keeping it under wraps.
3) The occasionally present ReconxSuguha vibes that showed up now and then kinda blunted the blow, I guess I'm just a sucker for an underdog.
I mean it gets teased enough that if it's a hot-button issue for you you might want to avoid it, but from a second run-through standpoint it definitely felt much more like a
Tropes are Tools instance of them having fun teasing ship bait for the shippers than anything that was ever intended to seriously evolve.
On the other hand a lot of the things that got me the first time around were just as good (well, bad) as the first time around. The nigh-rape scenes still held just as much of an emotional slime as before, and the seriously-charged moving moments held just as much momentum as before.