I've never seen the original Wrath of Khan so I didn't know about the ending being the same except for reverse roles, so that didn't bother me.
There were some stupid plot things, but I only thought about them after the movie was over, with the exception of Bones injecting the animal thing with Khan's blood and the Old Spock thing.
They were all busy getting ready, but then Bones is like, "hang on a second. I'm going to inject this human blood into this animal for some reason." It telegraphed super blatantly that A) the blood can bring things back to life, and B)someone was going to die.
And I just don't understand the point of the Old Spock scene.