The Enterprise under water scene is made more absurd because they made this Enterprise a lot bigger than Kirk's. It's about as long as a Sovereign at 700m.

As for the Klingons, both DS9 and Enterprise made it canon that they were smooth forehead like we saw in TOS. And, they showed by the models at Buckaroo Bonzai's office that Enterprise was still part of that time line.

Speaking of the models, what kind of super secret organization has a model of their newest super secret dreadnaught sitting out for everyone to see? And I'm sure you can buy the model at the Starfleet Command gift shop (and you'll be able to buy the model courtesy of QMx who made those models for the movie).

The Enterprise under water? Ok I know that Voyager was capable of this but really what was the point? What was wrong with being up in orbit?

Spock wigged out a little too much. Yes it's ok for Spock to periodically lose his composure it happened in TOS when he thought he'd killed Kirk and while the "Khaaaaaannnn!" emote did draw a rather ironic parallel it felt a bit contrived.
Khan was cool and I was surprised having read very little about the plot prior to seeing the movie but Khan Noonien Singh was supposed to be of Indian descent, not Anglo-Saxon.

I was pretty sure that was Praxis as well and it's entirely possible that in the alternate timeline increased military production over the last 30 years caused Praxis to destabilize sooner. It would also explain why Ketha province (Where Martok is from) is now a post-apocalyptic wasteland.

I liked how they did the Klingons and hope that the next movie involves an all-out war with them because the Organians aren't stepping in to stop the fighting and force a peace treaty.

Mentioning Section 31 was pretty awesome and fits with the more militaristic Starfleet of this alternate timeline. Some of their technology strains credulity though. If you can create a portable transporter that can beam you across hundreds of light years to your most fearsome enemy's doorstep then why not send a legion of Maco's to attack Kronos or any other strategically important planet?

I liked the reverse death scene and the parallels to TWoK that it drew as well as all the other little tidbits like Mudd's ship but point of order; Mammals have litters, reptiles don't. Gorn lay eggs it's in the cannon for heaven's sake.