"Know thy enemy, know thyself, know victory."
As tactical advice, Sun Tzu's famous maxim applies to a majority of videogames. Knowing that Piston Honda blinks just before throwing an uppercut helps you know victory. Knowing that the mothership fires two small shots before throwing up its shields helps you know victory. Knowing how many whip strikes it takes to defeat Dracula helps you know victory.
But what about the kind of knowledge that transcends the tactical - the kind of knowledge that lets you truly understand your enemy's motivations and background, his hopes and fears? As far as most games are concerned, such knowledge is unimportant. The enemy exists only as a part of the environment - a set of pre-programmed rules to be figured out and bested. It's enough to know that Piston Honda wants to send you a "TKO from Tokyo" or that Cats thinks you have "no chance to survive make your time." We want to know the enemy, just not, y'know, personally.
This is in stark contrast to other forms of storytelling media, which routinely include antagonists that are known for more than malevolence. Conflict is inherent in every story, but most well-told tales are not just a simplistic battle of good vs. evil. A hit TV series like Friends might feature characters with competing goals, but there are no characters that are completely morally reprehensible. A hit game series like the Mario games, though, can get by for decades with an antagonist that kidnaps royalty and casts destruction upon the land seemingly out of sheer boredom.
Even in stories where there is a clearly-defined evil, we can usually understand the bad guy's motivations, even if we don't agree with their methods. Most viewers can at least relate to the revenge and greed driving Simon Gruber in Die Hard: With a Vengeance, even if we would never attempt murder and massive theft ourselves. Other stories actively encourage the audience to root for the bad guy, finding the underlying humanity in normally vilified characters like mobsters (The Godfather) or psychopaths (The Silence of the Lambs).
As a medium, games are different in this regard. In games, the bad guy is, almost by definition, the one you're not controlling - the "other" that is trying to destroy or limit you. If you're controlling a cop, the gangsters are the bad guys. If you're controlling a gangster, the cops (and, sometimes, the other gangsters) are the bad guys. There is no moral ambiguity - most games are designed so it's you and your character(s) against the world by default.
No wonder so many game makers create paper-thin, cartoonish justifications for their virtual enemies. No matter how well-defined and believable a game villain is, his motivations will almost always pale in comparison to that of the protagonist you're actively controlling. Knowing the misunderstanding that causes Sephiroth's psychosis and rage in Final Fantasy VII doesn't prevent you from preventing him from destroying the Earth in the final battle. Knowing that Otacon will be crushed by the death of Sniper Wolf in Metal Gear Solid doesn't give you the option to spare her life and sit down to a tea party.
Like a Greek tragedy, most game narratives march inexorably toward the final condition of "you win" regardless of what this might mean to the fate of a likable, non-playable bad guy. Given this inherent rule of standard game design, the question regarding enemies becomes not "Why are they doing this?" but rather, "Do we really want to know?"