The main criticism I keep hearing and reading about Star VI was that the Cold War analogy was too obvious. I've never really understood why that is an issue.
The end of the Cold War was obviously a massive event at the time and it is not surprising that films ended up using the theme and trying to send a message.
Why is it such a problem that it was rather obvious? I think it would've been a problem if they had just taken a random theme and forced it into a Trek movie but that's not what happened. I thought the whole movie actually worked quite well. The old heroes who had been fighting Klingons on and off all their lives, there was indeed a Cold War, the end of a generation (the crew retiring, but also Galactic politics changing big time). I thought it all fit the narrative really well. I think it served both as a wonderful send-off for the old crew and also as a turning point that worked to foreshadow the events in TNG (which obviously was already running at the time). That whole "getting old" theme had already started in TWOK and came to a conclusion here. Our heroes weren't just getting old, it was also the world that changed around them big time. In the end they manage to adapt and hand over the torch.
TUC is probably my favourite Star Trek movie. I like the mood, the dinner aboard the Enterprise, the political aspects, the adventure.
I thought the Cold War analogy was no more obvious than all the Moby Dick references in TWOK, frankly. The analogy wasn't enough to take me out of the movie, so to me it felt better integrated in that sense -- I only think about the analogy after a viewing, once I've had time to analyze it myself.
With that said, TUC is pretty much the only movie that I'll definitely stop and watch if I'm channel surfing. Maybe FC or '09 once in a while, but TUC is definite.
On a side note, while channel surfing this weekend, I discovered VH1 playing TSFS. I'm all for more Trek movies on TV, but... that movie has nothing to do with pop and adult contemporary music, right? Unless the Mos Eisley Cantina scene was a bigger hit than I realized...