I think part of it is that EY writes for fun, rather than solely with some direct aim in mind, and he really likes stomping on landmines. (And who can blame him? Stomping on landmines is fun!) The fic includes a fair number of things that his average audience member dislikes, but which is there because he likes it, and would likely be unable to write as much if he kept restricting himself. There's a reason that there's a significant word count devoted to anime references, and I believe it's mostly related to what produces hedons for him.
My bet is that the last bit will be polyamory in the epilogue.
See here for a thread posted shortly after chapter 115:
It was an excuse to have two characters talk about the plot - doesn't seem like there was anything more to it.
The solution was actually posted to reddit after chapter 112, before there was a final exam at all.
The big problem is that he left Harry his wand. If he uses more precautions against Harry, but still keeps leaving Harry his wand, then that makes the fact that he left Harry his wand less realistic, not more. So I actually think that you should go the other way with it - have him be less paranoid about Harry. Because otherwise you're making the inconsistency even worse. He's being cautious and paranoid enough to strip Harry's clothes from him, but leaves the wand in Harry's hand for one moment longer than he has to? It makes more sense if he has the Death Eaters throw a bunch of Finites at him to check for residual traps left by Dumbledore, and for that to be where he sees most of the threat coming from.
Planning thread over at /r/HPMOR for centralized discussion. It's probably better to have segregated groups working on this, but I don't really think that'll be a problem.
It's still a matter of limiting the mileage. Even if there is no formalized and ready-to-fire response (one that hasn't been written in the heat of the moment), there's always an option not to engage. Which is what I said last time he engaged, and before he engaged this time (and also after the fact). If you engage, you get stuff like this post to /r/SubredditDrama, and comments about thin skin that not even Yudkowsky really disagrees with.
It doesn't take hindsight (or even that much knowledge of human psychology and/or public relations) to see that making a twelve paragraph comment about RationalWiki absent anyone bringing RationalWiki up is not an optimal damage control strategy.
And if you posit that there's no point to damage control, why even make a comment like that?
It's not a matter of "winning" or "not winning". The phrase "damage control" was coined for a reason - it's not about reversing the damage, it's about making sure that the damage gets handled properly.
So seen through that lens, the question is whether EY is doing a good or bad job of controlling the damage. I personally think that having a page on Less Wrong that explains (and defangs) the Basilisk, along with his reaction to it and why that reaction was wrong (and all done with no jargon or big words for when it gets linked from somewhere, and also all done without any sarcasm, frustration, hurt feelings, accusations, or defensiveness) would be the first best step. I can tell he's trying, but think that with the knowledge that the Basilisk is going to be talked about for years to come a standardized, tone-controlled, centralized, and readily accessible response is warranted.
"Damn the consequences" seems like an odd thing to say on a website that's noted for its embrace of utilitarianism.