If it was not for the need to have a fallback for IE9 I would be using flexbox as standard, its a great feature with deals with so many of the common page layout issues, including vertical align.

Bootstrap is quite web focused still so I guess it will come when support for IE9 is not expected.

Though if you are doing an mobile/tablet only solution I would probably use flexbox only now. As long as you keep to the 2012 spec, you should be ok.

http://caniuse.com/#feat=flexbox

Bring on the death of IE9!!