So, once you get used to how it works, you can get done what you need to get done. I'm pretty clueless when it comes to domain names, but whenever I've been going through tutorials on websites, the settings I need to change have been there in GoDaddy, so that's a plus. At least they're not missing anything I need through all that clutter.
Based on that, I chose to use NameCheap. I've been happy with it so far.
I'm not 100% happy with them either - they are definitely clunky as all hell. Lately I've just been setting my default nameservers to Slicehost and using their domain management tools for setting up zones and records, which at least lets me avoid some of the annoyances of Godaddy.