The prison they were keeping Cobra Commander and Destro in was kind of cool. 12+ miles below the surface, thus technically being outside of any national borders, was a nice touch. The drug they used to keep the prisoners passive; cool. The kinetic kill weapons in orbit; fucking awesome.
But then they had ICBMs that can travel from the USA to all of their targets in 3 minutes? Yeah, multiply that by 10 or 15. Apparently the writer was completely ignorant of something called "second strike capability", which means that after an aggressor fires nukes at you and hits targets, that's when your subs launch their missiles and waste the country that nuked you.
Fuck, I almost forgot! The fight scene between Storm Shadow and Snake Eyes in the mountain keep... Storm Shadow is throwing ninja stars at Snake Eyes down a hallway and Snake Eyes is fucking shooting them out of the air with a sub-machine gun, but completely misses hitting Storm Shadow? I almost broke my eyes from rolling them so hard.
The cliff side ninja fight is by far the best part of the movie, and you've probably already seen it.