Don't view Bootstrap as a choice. Tim Medora made a lot of good points. But I would note that it's always possible to pull individual pieces of Bootstrap and to customize aspects of it to get something that looks fresh, either by digging into the code or using the homepage's customize page. Sure, if you keep the basic navbar and menus, you're going to get something that feels very conventional, and that may be a problem. But lots of people have used Bootstrap to make unique looks.
It's perfectly acceptable to use the grid system but design your own components. Or ditch the grid and use their components. It's not an either/or proposition. The only time it really gets tricky is when you decide you really want to change something, like the look and feel of a menu. The "right way" to do it isn't always readily apparent. You may have to dig pretty deep into the code, and it can be tough to make sure you're changes aren't breaking something else. But that's still better than not having an example to pull from at all.
I think the only mistake you can make is not taking a thorough look at what Bootstrap can provide you.
