About two years after revision 2, I decided to do a complete redesign of the board. The general form factor stayed the same, but many of the original design's issues could be addressed. Most importantly, revision 3.0 features an optimised prototyping area. Here's what it looks like:
Schematics, layout and code examples can be found on GitHub.
There also is a blog post with details about the whole development process, including a list of all the changes.