We don't really have any plans for more extensive/easy cart customization options than what's already documented here:
http://www.e-junkie.com/ej/help.custom-cart.htm
You can already do quite a lot with some clever use of CSS, which the overlay cart inherits from your own page/site (since the overlay cart basically renders as a set of extra DIVs "inside" your page). To see how the cart is structured and figure out what you could do with CSS, paste the URL of an Add to Cart button into a blank window/tab and View>Source on that. You can even copy and paste that source into any HTML editor you're more familiar with, which would give you nicer syntax highlighting and code-reformatting options (fully hierarchical indenting could be handy for analysis :^).
One REALLY handy tool we've found is a Firefox extension called View Source Chart:
http://jennifermadden.com/scripts/ViewRenderedSource.html
It does cost $10 for the Firefox 3 version but IMHO worth every penny (and you'd also be supporting a fellow E-junkie Merchant! :^). Using this tool, you could View Cart in the standard overlay fashion and then View Source Chart to see our DIVs and other wrapper code which the browser adds to the end of your own page source when you invoke the cart display, then tailor your CSS as needed.