I mean, in the movies, "Lord of the Rings" they connected the snow storm to one of the villains and it was just a freaking snow storm, because of the time of year, not the villain.
I will point out that in the movie, Saruman explicitly summoned the snowstorm to prevent the fellowship from having a comparatively easy way around a potentially dangerous location. The main characters were not stupid, especially Gandalf. Hell, he could have made it so there would be no snowstorm to stop them. As shown prior in the film, Saruman had defeated Gandalf, who only escaped because he was fortunate.
That aside, you do raise excellent points. A lot of people seem to ignore pragmatism when it comes to villains an antagonists. Unless the method for summoning the bigger bad requires causing as much chaos as possible, there's little reason to have your hand in everything unless you're explicitly against the main characters or those places had something you needed.
As a counterpoint, more of an examination for reasoning, having a single villain is more simple, it's something you're guaranteed people will understand, even if the overarching plot is a bit more complex than people are prepared for. I'll raise an example of multiple villains in a movie: Spiderman 3, which had Venom, Sandman, and Green Goblin as primary antagonists. The more villains you have, especially ones who are not explicitly working together, the longer the story has to be to make sure all of their stories are fully fleshed out. It's not considered a good movie because all of these plotlines clash and mingle in various different ways.
In movies, having a more complex villain or group of villains makes for a longer, more complex story. Movies are generally constrained to a certain length, and if the people paying for the movie being made are not sure a longer movie, even a multi-part movie, will be accepted by the general public, they won't support it and make it shorter, thus making it impossible to fully explore the themes of the story. Games have more freedom in that regard, they can have as many disks as needed to explain the story, but again, are constrained by the people paying for its creation. Thus, the problem becomes two-fold: Too much complexity can turn away the people for whom the story is being told, and can have the people paying you for making the game in the first place force you to make the game simpler, if you rely on their cash to make the game.
Another factor: people like consistency. If a player has to wade through multiple mini plots to attain a single goal, they'll accuse the game of being unfocused. With this lack of focus, they lose interest or lose track of what's going on. Thus the problem become three-fold: Lack of interest, players telling other players not to play the game because nobody knows what's going on anymore.
Having a singular overarching villain makes things simpler, easier to follow. Having more villains, especially ones that aren't explicitly working together, calls more more complex storytelling.