In the run up to the release of New Super Mario Bros. Wii, Shigeru Miyamoto mentioned that Princess Peach wasn't playable in the game because it would have been too difficult to animate her dress.
The programmers behind New Super Mario Bros. Wii aren't the only ones who find skirts problematic, it seems. In a recent interview with Famitsu magazine, The Legend of Zelda: Spirit Tracks producer Eiji Aonuma said the following when asked about Zelda's appearance in the game:
"People on the staff have wanted to have Zelda in the game for ages, but if we did that, then her skirt becomes an issue. Having girls in dresses in an action game is kind of hard to deal with. That's how we got the idea of having her body stolen and her soul going inside Phantom Guardians."