In addition to what Hristo said I would like to add
I cant argue with the above, most of it are true, however it applies to all third party packages that nop commerce uses. U can write jquey or any other package but u still use it.
there are many advantages using bootstrap I thing its perfect for a project like nop commerce that most of the community are .net developers and not designers.
I find bootstrap very easy and useful with a lot of online support and themes. I think the default theme have to be done with bootstrap since it a simple structure to design a complex theme on top of it.
I would vote for bootstrap as the default theme, I think it is a must