There are three objectionable aspects to villains, not just in Star Trek, but any and all movies.
First, basically nobody thinks of themselves as a villain,
not even the cool bad ass dudes who revel in kicking ass. The villains who enjoy twitting the heroes with their glorious badness are basically a joke, even if the actor can manage to project menace. (This is especially true if the audience is kind of gullible. It's why Ledger's Joker is not an amazing performance. Remember the Joker instead of Ennis makes a laughingstock of Ledger's life as an actor.) The psychopaths who really don't have any morals don't usually have any sense of humor either, nor are they magically gifted with really cool style. Generally, their life strategies involve mimicking normal people with consciences, not enacting vicarious fantasies about doing what you want.
Second, the notion that making it personal makes it more intense usually fails, because more personal is usually more petty.
Worse, the number of ways to make it personal is pretty limited. This means making it personal demands anchoring the plot on a cliche,
which is not good.
Third, making the plot about resolution of physical jeopardy is melodrama, not drama. Drama is about choice. A physical jeopardy plot usually ends with a combat, even a hand to hand combat. But this is not more intense, even when the plot doesn't have to be contorted to set up the final confrontation. There isn't much drama in a protagonist choosing to fight to live or save someone,
because it's an easy choice to make, however hard it may be to execute. "Does the hero win?" is hardly worth asking yourself.
Unfortunately, you can't escape the fundamental second rateness of the hero vs. villain structure simply by maintaining there are no villains nor heroes, that it's all shades of grey or moral ambiguity. A drama without a point of view is, well, pointless.