I'm attaching a patch I've made to Video Filter 7.x-3.1 to allow the passing of additional parameters to YouTube clips (loop, modest branding, controls, autohide, showinfo, theme, color).
The patch also addresses some issues with video heights/widths being calculated - the 7.x-3.1 branch was incorrectly using the $filter->settings array for data rather than calculating height and width based on the supplied height/width and ratio values.
Please assess this against your branch and take what you need from it.
I needed looping YouTube video with no YouTube branding, hidden controls, and a height calculated based on 16:9 ratio and set width which the 7.x-3.1 branch could not do.
Using this patched branch I can use the following input text:
[video:http://youtu.be/aGPTVMaMfn0 width:672 ratio:1280/720 autohide:1 modestbranding:1 controls:0 control_bar_height:0 loop:1 showinfo:0 autoplay:1 theme:light color:white]