The antagonist. The big boss. The Foozle. Whatever you call the bad guy of your favorite video game, chances are, if you like the story, you think the bad guy was awesome. Is there a fan of Final Fantasy VII who doesn't worship Sephiroth's bangs? While people like me, who prefer FF6, also prefer Kefka as a bad guy. And my favorite console RPG, the aforementioned Suikoden II, has my favorite bad guy combo with the pure evil Luca Blight and the idealistic antagonist of Jowy.
It's not difficult to explain why the bad guy is the driving force behind game plots. It's because game stories are driven by conflict, almost always between good and evil, and almost always, the good guy is really freakin' boring. There's basically two types of good guy in games, the idealistic teenager and the not-very-reluctant-fighter. Honestly, how long does it take Cloud Strife to go from being an amoral mercenary to Hero of the World? About 10 seconds?
In games, however, often the antagonist - the character whose conflicts the hero provide the game with focus - differs from the big bad guy - the being which must be defeated at the very end of the game (CGW's former RPG guru Scorpio entertainingly named that big bad guy "the Foozle".) For example, in the charming Saturn/PSX RPG Grandia, the main character's antagonist is the not-evil Col. Mullen, who must eventually realize the error of his ways. In the first half of Warcraft 3, the antagonist is also the protaganist, the tortured Prince Arthas, though this kind of antagonism is an extreme rarity, especially done well.
The focus on the bad guy as the driving force behind a game's plot also helps to explain why game plots are so weak. It's because their bad guys are weak. For a bad guy to succeed in an overdramatic setting, like games almost always are, they must either be remarkably human, or remarkably inhuman. A human enemy creates empathy and sadness, or at least understanding. An inhuman enemy can create fear and hatred.
I call this split the Iliad/Odyssey methods of storytelling, which should serve as a good set of examples. In the Iliad, Achilles is the protaganist, and is a big jerk, but a recognizably human jerk. Hektor, the antagonist, is the most sympathetic male character in the story. Hektor must die, but when he does, it is a tragedy.
In the Odyssey, the antagonist is no longer a person, but the forces of nature anthropormphized into Poseidon, the ocean god. Odysseus struggles against not recognizable humans, but dangers in the form of monsters and natural distasters.
Most games lie between these two extremes. Game villians are generally forces of nature forced into the weak flesh of humans, like the pure evil of Sephiroth whining about destroying the world for no readily apparent reason. Or they are humans with inhuman motivation, wanting to destroy the world just because they felt like being evil one day, or like in D&D, they have an evil "alignment". This is ludicrous, of course, the great villains of human history always believed that they were doing good.
There are a few exceptions, but they are rare. Primary in these has to be Ultima VI: The False Prophet. In U6, the game world's humans are involved in a destructive war with the gargoyles. In any other game, the main character's quest would be to fight gargoyles until they got strong enough to defeat the Gargoyle King and save humanity. In Ultima 6, however, the quest is to first remove the gargoyles from the main battle lines, then to learn to understand them, then to bring peace and save the gargoyles from destruction. That's right, a game where you win by STOPPING violence. Shocking, and never repeated.
There's also the Fallout-based games, which offer the choice of good or evil. These include Baldur's Gate, Planescape Torment, and Knights of the Old Republic. By the player's choices, the main character becomes good or evil, depending on how they solve certain quests. However, generally speaking, these games still have basic antagonists to fight against, only the form of that battle changes with the player's choices.
Until game writers start to form human bad guys who draw the gamer's sympathy, or pure evil bad guys who draw the gamer's hatred, then there's no real reason to worry about bad guys. After all, we know that the world is going to be saved. But if it's a battle for your enemy's soul, or a battle to prevent the bad guy from destroying everything beautiful...then, then we can care.