The problem with bootstrap is only a small portion of it's design aspects can be changed. This is a problem with the way they've (not) used LESS. The only variables are colors and the font. Options for sizes, spacing, some layout options how you want to the topbar to work are all much more limited and harder to do. So for the most part aside from color, if you are using bootstrap it's going to look like a bootstrap site.
This is fairly different from say Blueprint/Compass where almost anything can be tweaked just with SASS varaibles.
But the whole point of Bootstrap is for _non_ designers to be able to make decent looking sites with minimal effort. Give them control over things like spacing and font sizes, and most of them will get it very, very, wrong.
Well, the grid system of bootstrap could be used for a lot of wrongness, but by then you'd be avoiding most of its base system anyway and could do the same amount of damage with any kind of simple CSS grid.
I'd go a step farther and say that even the little bits you can change are prone to abuse and/or simple hard to get right for a number of non-designers. The generator system above actually just fills in some blanks, which isn't exactly the difficult part for programmers. It's what you fill in those values… My idea for some part of "custom" generator would be selecting a palette from a reasonable large number and then probably some basic font types and weights, similar to type-a-file[1]. Then add some customized icon set[2][3], and you've got something that's at least a bit more unique.
This is fairly different from say Blueprint/Compass where almost anything can be tweaked just with SASS varaibles.