As of WordPress 3.6 you may now modify the passed attributes for any shortcode (that supports it) via a filter.  Here is the filter:

shortcode_atts_{$shortcode}

where {$shortcode} is the id given to the particular shortcode you’d like to modify.  In this example I am overriding the embedded video width and height to force it to a specific size:

Any video embedded via the shortcode will now have the dimensions of 768×583.