This Trek film could have been titled, "Star Trek IV: Attack of the Alien Whales".
Why are there so many films and episodes where an unstoppable force heads right for Earth and nothing seems to be able to stop it? Why? Because the writers have so very little creativity left in them after writing so many stories over the years.
This film was written specifically to bring the plight of the whales to mainstream audiences through a light-hearted Star Trek film. Yes, there are a few laughs, but this is just a sign that Star Trek has become nothing more than a joke. This concept may appeal to Trekkies (which is why ST: 5 was only appealing to Trekkies and universally hated by any other human trapped inside the theater) but it serves to damage the franchise further. The end result was that the last ST film basically bombed at the theater.
So, yes, you can trace the loss of Star Trek's appeal to films like this one.
As for the special effects, there are very few at all. There was one weird sequence when the crew was traveling back in time, which had to be the dumbest segment in sci-fi history.
If you really feel you need to see this film, watch it for the laughs, not for the sci-fi value, because there is little to none of that.