Metro UI does have gradients and drop shadows, though they are very subtle.
If you are good at design, you wouldn't need to start from Bootstrap. If you are not so good at design, Bootstrap is a great framework, but using flat, all-square UI elements can cause some problems, you may be unaware of.
If you use Flatstrap, your tags, labels and buttons will all look the same. If, in the spirit of flatness, you'd also removed the inset shadow on form inputs, then all visual cues for either clicking (element is higher than the page) or form input (element is lower than the page) are gone. This reduces usability and discoverability. [1]Rounded boxes serve another function, where they draw the attention of the eye to the contents of the box -- It flows more pleasantly too [2]
Designers going for the flat design trend, should carefully strike a balance between a completely flat design, and using subtle gradients, underlines, rounded corners, color, shadows and pseudo-3D to convey information that matches our expectations and wiring of our brains.
[1] http://www.useit.com/alertbox/windows-8.html Flat styles reduce discoverability
[2] http://uxmovement.com/thinking/why-rounded-corners-are-easie...