Reading some of these responses makes me think that most people weren't exactly paying atention to the movies while they were watching them. ALL the antagonists had proper motivations (even when there were no "villains", i.e. I, IV and V).
The Motion Picture - V'Ger was like a child. An old Earth probe that was converted and upgraded by artificial intelligence on an all-machine planet that was on a quest to return "home" and join with its creator. Not evil. Not malevolent. And really only becoming truly threatening when perceiving a threat from an outside force. It didn't travel to Earth specifically TO destroy the Earth. That was just an unplanned consequence when it didn't find what it was looking for initially. Once Decker joined with it, thus providing V'Ger with a "creator" figure... BOOM! Threat gone.
The Wrath of Khan - The most personal villain storyline, but really only if you're familiar with the original series episode "Space Seed". Khan and his followers were late 20th Century genetically-engineered supermen who, when brought out of their centuries-old hybernation continued their bred-in ways of conquest and became a threat to the Enterprise. Kirk, rather than killing of imprisoniong them, found a suitible planet for them to colonize where they could presumably do no harm. In between the episode and the movie, a neighboring planet exploded, the shockwave laying waste to the paradise-like planet Kirk had selected for them and killing most of Khan's followers including his wife. For Khan, the only thing that mattered was revenge against Kirk. The Genesis device was just icing on the cake to him.
The Search for Spock - A Cold-War metaphor to the arms race. A renegade Klingon commander sees the Genesis weapon as an all-powerful WEAPON, not a device used to create new worlds. He is seeking to gain control of the secrets of this weapon to level the playing field between the Klingon Empire and the Federation.
The Voyage Home - Another non-villain story, where a probe was sent seeking to find the answers as to why Humpback whales were no longer in communication with them. Here, the plot device was solving a problem, not fighting an enemy.
The Final Frontier - I don't consider Sybok to be a villain, as he really wasn't trying to attack or kill anyone. He was merely a religious fanatic who wanted to meet God and prove that God exists. Once he proved the barrier could be breached, he immediately relinquished control of the Enterprise back to Kirk. (The Klingon "villain" motivation was TRULY pitiful, though, and entirely unnecessary except as a weak attempt to try and show the roots of the Federation-Klingon truce now that The Next Generation had started its television run. This was a plot idea that was MUCH beter explored in the next movie.)
The Undiscovered Country - Another Cold War allegory (something Star Trek has EXCELLED at over the many years). "People can be very frightened of change"... so they had their motivations for trying to stop peace talks from occurring.
Generations - This one REALLY interests me, as it is a great twist on drug addiction. (Whoa! What???) Yep. Drug addition. Listen to Guinan's explanation of what the Nexus is. It is a place of infinite joy. Soran was ripped away from the Nexus involuntarily by the Enterprise B, and he was willing to do anything... ANYTHING... to get back to that place. It didn't matter what he destroyed or who he killed, he HAD to get back there.
First Contact - No real moral to this one. The Borg were facing a long and heated war with the Alpha Quadrant and figured the best way to win was to go back in time and stop the Federation from ever being formed. Want a REAL interesting take on this one? Picard's underlying motivations essesntially became those of Khan's. Was Picard a villain, then?...
Insurrection - This is the only one I don't truly get. With only a couple of hunderd people on the planet, why couldn't the Son'a simply SHARE the planet with their Ba'ku relatives? Surely there had to be enopugh room on AN ENTIRE PLANET to be how they wanted to be differently and not have contact.
Nemesis - A morality play on the nature of duality and how it is our experiences that form us, not genetics. Shinzon essentially wanted to be the Abraham Lincoln of the Reman race, freeing them as slaves, but harsher. He wanted to punish the Romulans for the treatment of the Remans, and in order to extend his own life, he needed a complete blood transfusion from the original Picard. What exactly his beef against the Federation was remains the weak link to his motivation.
Star Trek - Nero was another Khan-like villain whose motivation was revenge... this time against Spock, for failing to prevent the destruction of his homeworld, Romulus. All that mattered to him was making Spock endure what he himself had to endure: viewing the destruction of his home. However, just as with Shinzon, why he felt the need to go after the Federation as well... who knows?
So each villain (or antagonist) had very pronounced and clearly defined PRIMARY motivations. In the later movies it was the secondary ones that appeared to be somewhat of a hindrance to the telling of the story.
