You can't patent Colors / Helvetica Neue / Rounded Corner Squares. It just reeks of tactics similar to patent trolls.
I think a while back there was blog theme used that was similar to Svbtle, but there was no take down notice or such nonsense. It generated a decent discussion and conversations about something that's too close in style.
Look at @layervault on Twitter, they are just getting destroyed right now. Even by designers, their main target audience.
If they went along the lines like 'Hey, this is pretty similar to our design. We think it's cool we inspired you but can you deviate it from us a bit more or re-name the project to like Layervault Bootstrap?' I mean why not - have your name in the same conversation as Twitter Bootstrap!
A total botched and missed opportunity.