You mean where the roles of Kirk and Spock got reversed? That was a little strange and I did think that Kirk was going to stay dead. But I had not figured in 'Khan's regenerative blood' aspect as well as using one of the cryo-tubes to keep Kirk from lapsing into death even further. I also think the USS Vengeance could have used more air-time. Unfortunately given the fact that it was too powerful a star ship, the Enterprise would not have lasted long enough to give us a good battle like it was with Star Trek II's Enterprise Vs Reliant. I actually liked the Vengeance design. and given the fact that it is purely a military ship I could see her lasting for quite some time against a Borg cube ship. I'm also betting that she could hold her own against Nero's ship; The Narada.
Yeah I heard that "Khan's magic blood" was a cheap deus ex machina at the end. Again haven't seen the movie but it just seems like a bad idea to intentionally invite direct comparisons between your new movie and what's been nigh-universally regarded as the best film in a series for decades.
A warship huh? I'm not really sure how prominent ships built purely for fighting are in the history of the federation in the original "prime" timeline, so that might mark another significant diversion. When the USS Defiant was introduced it's conflicts with peaceful, exploration-based ideology of the Federation is brought up. And as a warship it's said to be unique in Starfleet at the same time. But I guess there must have been at least a few warships back when fighting the Klingons was a regular occurrence.