Below are simple styles to "flatten" bootstrap. I didn't go through every control and widget that bootstrap offers, only what was required for https://commando.io, so your milage may vary.

bootstrap.flatten.css

/* Flatten das boostrap */
.well, .navbar-inner, .popover, .btn, .tooltip, input, select, textarea, pre, .progress, .modal, .add-on, .alert, .table-bordered, .nav>.active>a, .dropdown-menu, .tooltip-inner, .badge, .label, .img-polaroid {
 	-moz-box-shadow: none !important;
	-webkit-box-shadow: none !important;
	box-shadow: none !important;
	-webkit-border-radius: 0px !important;
	-moz-border-radius: 0px !important;
	border-radius: 0px !important;
	border-collapse: collapse !important;
	background-image: none !important;
}