If the Klingons were capable of building a prototype super-bird-of-prey, then they were capable of building more. That would seem to be a galactic game-changer. Why did they not do so?
It could be that before it went into mass production, the technology had already been rendered obsolete.
It's possible that the exhaust vulnerability that the Enterprise crew was unavoidable, and since the cloaked ship had to have its shields down it was also vulnerable, so that in the end it was more tactically advantageous to have uncloaked but shielded ships than cloaked but unshielded ones.
It could also be that by the time they solved that problem, the Federation had already developed sensor technology capable of detecting ships using this prototype technology.
Plus, with the Khitomer Accords in palce, perhaps the Klingons invested less in military development, thereby letting the project go into mothballs. Heck, a certain level of deinvestment might even have been a part of the terms of the treaty, or it might have been done as a goodwill gesture.
I never understood how Kirk formed such an attachment for David Marcus when he barely got to know the young scientist. He asked Carol: "Is that David?" and yet in TUC, he mourns the death of "my boy", a son he never knew.
Yeah, I really loved what TUC did with Kirk's previous experience with the Klingons, but unfortunately the build-up provided by previous movies wasn't great.
When watching either TSFS or TUC, I like to pretend that Kirk had a great relationship with David in between TWoK and TSFS, even if that isn't supported by the on-screen evidence; it makes the movies that much better.
In the beginning of TUC, we hear Sulu's log aboard Excelsior, about how the ship just finished cataloguing gaseous anomalies. Yet during the battle over Khitomer, Uhura brings up that Enterprise-A is carrying the gaseous anomaly-cataloging equipment. But was there ever a hint that Enterprise-A was doing the same work as Excelsior? I don't think so.
According to George Takei's autobiography,
To The Stars, in the original script it was the Excelsior that shot down Chang's ship in the end, but Shatner requested that it be rewritten because Captain Kirk shouldn't need anybody else to come rescue him.
Takei probably isn't the most objective of sources on William Shatner, but it does sound quite plausible. In any event, it's a shame the Excelsior didn't get to fire that shot; it would have been an awesome way to show how even as the Enterprise-A is about to be decommissioned, the adventure lives on through its former crewmembers.