One thing that is important, at least in the wall module, it to move js calls from the classes to the template files so that the js can be overridden with a template change. For instance, outline.js is loaded from BxWallModule.php and the width of wall items are set by:
$(document).ready(function() {
$('#bx-wall-outline .wall-outline-items').masonry({
itemSelector: '.wall-oi-item',
columnWidth: 170,
gutterWidth: 20
});

All the positioning of outline items is derived see more from this, and template designers are stuck with it... unless we alter source files. If that small amount of js is moved to the template html files, all of the outline can be changed via template. This small change will allows a template to detect a mobile browser, and change the outline items to better adapt to the small screen.

I haven't dug into other modules, but the wall module is the most critical. If there are other module classes that load js that affects layout, it would be advantageous to move that js to template files as well