Personally, I've never had a problem simply ignoring the features I don't need. Nevertheless, this is a frequent request. If you're sick of waiting 10 minutes every time you want a new top-level folder, Paul Hacker has a solution for you: Empty Process Template. It's not completely gutted, but it should cut down the amount of overhead associated with each Team Project.
Paul's blog is probably the best place to leave feedback. Enjoy!