I have run into several cases where jQuery packed has caused issues in browsers (document.ready and curveycorners), so offering jQuery minified shouldn't be too hard.
You can add option of the CSS based layout, 3 column, 2 column etc.. and also include the common elements in header.php footer.php etc.. it will be really cool if you can do that.. it's there on http://csscreator.com/tools/layout
The more options the better! Adding access to different Javascript libraries like MooTools and script.aculo.us only opens up this great tool to tons of different developers who happen to use different frameworks