I never wrote a Baskerville reaction post, so let me get my thoughts out now before we all get Reichenbach'd in 4...3...2...1...
I had basically two reactions to The Hounds of Baskerville (not counting OMG Captain John Watson!), plus one meta-reaction to everyone else's reactions. The first basic reaction was horror at the let's-experiment-on-John part. Specifically, I reacted poorly to the flashback scene where they show us Sherlock sitting at his ease watching John scurry around like a lab rat, not to the fact of Sherlock's experimenting on John by itself. When they sprung that on us, it felt like a ship-killing moment to me. But I've been in shipping fandom for 15 years, and I know by now there is no such thing as long as the goggles are strong. Fic therapy is already helping.
My second reaction is much more complex, and is as much about Scandal as it is about Hounds. (Scandal left me with much, much more to think about!)
At the end of Scandal, I was appalled at the length of time they'd allowed to pass since Irene's resurrection without showing us any cases, any joyful moments, or John's progress in coming to terms with Irene's words at the power plant ("Yes you are," "Look at us both."). I was particularly put out by not knowing how John was left thinking about things at the end of the ep. Leaving aside the fact that they've jossed their own timeline on
http://johnwatsonblog.co.uk/, throwing the six months into question, I had overlooked one vital clue: John's last conversation with Mycroft, in which he earnestly attempts to convince Mycroft that Sherlock is immune to sentiment: "He's not like that. He doesn't feel things that way, I don't think."
Watching him during Hounds, I got the sinking feeling that he really does see himself as largely in a caretaking role at this point in the series. He's one of Sherlock's handlers, which to me is not romantic in the least. And then I remembered that conversation with Mycroft. And at this point, I believe that canon John has considered any feelings that arose from the power plant conversation and set them aside as irrelevant, due to his having settled on an understanding of Sherlock which precludes Sherlock feeling attachment.
This, by the way, fits all too well with the (puzzling, to me) way in which John takes being experimented on almost in stride. If he thinks Sherlock is incapable of being better than that, then of course he puts up with it. And this, to me, drains a lot of energy out of the ship.
But fandom was split: half seemed to think Scandal anti-ship and Hounds bromantic and shippy, and the other half (mine) found Scandal very shippy if angsty, and Hounds to be ship-poison. Musing on this divide led me to my meta-reaction on these two episodes: for different fans, different things float their ships.
Some are bromance-heavy and for them, friendship translates directly into ship. They loved Hounds. Sherlock and John are out there working together, declaring friendship, going on a road trip! I enjoyed all that, but to me it read as friendship in place of ship-ship. It didn't spark. (BTW, if you loved Hounds and found it shippy as all hell, please tell me if I'm getting your viewpoint wrong here.)
Then there's those of us for whom shippiness comes from pining, frustration, worry, arguments ("Actual human lives!") - anything with very strong emotions, anything where they're clearly getting under each other's skin. There is (with goggles on) a lot of pining in Scandal. John's face as Sherlock is leaving the power plant is just amazing. Jealousy is shippy in this mindset ("Hamish.") Doubled-over-laughing is good too, strained moments of eyesex better.
My theory doesn't account for everything. If I like arguments, why don't the ones in Hounds seem shippier to me? There's loads of jealousy in The Blind Banker, but it always rang wrong to me despite the fact that that script should have been loads of shippy. The direction has something to do with it. A lot, probably.
So, Reichenbach is coming in two-and-a-half hours. It's a new director. Critical acclaim doesn't mean I'll like it. But you know why I'm not too worried? Because I ship angst. Cue the tears!