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 rem…
Just to nitpick, even if you're 'good' at design, Bootstrap is nice if you just don't want to spend the time for a prototype or small project, and also want to be able to drop-in different themes easily to test them out (ie, Bootswatch).
> using flat, all-square UI elements can cause some problems, you may be unaware of.
Remember that, in "true" Metro, all titles and elements are clickable, so the concept of affordance and discoverability is almost moot - its mere existence signals that it can be clicked on.
This is a a paradigm shift from what we've been using all our lives, so naturally people will need to adjust to it a bit, but I don't think it's fundamentally different from adjusting to clicking on rounded rectangles with dark edges instead of pressing a physical button.