I come away from STFS a bit confused about Katra-storage, ie is it a routine procedure for Vulcans (even if it's not normally put back in a cloned body!) and if so, why isn't Starfleet more aware.
Robert Comsol reminds me that Kruge's actions don't make a whole lot of sense. Still one of my favourite Klingons though, ruthless and a bit psychotic.
The bit about Protomatter was kind of un-ncessary. We could have believed Genesis was unstable - especially in a first uncontrolled planetary scale test without some secret forbidden ingredient. Maybe the writers wanted to give David a rash\risk taking side like his father?
Overall though I still find the film quite watchable. And maybe since I'm more aware of WoK's flaws these days (great film still, but, not great pacing) I find they fit together pretty well.