I have had a lot of fun following Ben Eater's[1] projects, which aren't always embedded-specific (sometimes they're TTL, sometimes Arduino) but are excellent for understanding concepts deeply.
I tend to learn best with a specific project that can grow or morph as my interest or experience dictates. You might find something to build with an Arduino, using the toolchain/IDE/libraries, get it working and then start stripping out libraries for your own implementations, or getting a toolchain of your own to cross-compile and flash.
[0]: http://www.edx.org/course/embedded-systems-shape-the-world-m...
[1]: https://eater.net/