I was almost tempted to vote for style, but I definitely have to go with functionality. Uniqueness is great and all, but it limits the types of levels that can be made and they will all basically look the same. Functionality is a JCS user's best friend since it's mostly up to that person to use the tileset to make a unique level.

Basically, style is good for making a few interesting levels and functionality is good for making numerous unique levels.

It should be noted that comparing functionality to style is like comparing gameplay to originality. Style is a part of functionality, and it doesn't necessarily denote how good a tileset looks.