Having many resources can be a bottle neck with theme develop, and a problem with having a performant mobile website. Optimizing your resources accordingly will give you the better chance of properly indexing your mobile site with google. Google has a crawl limit of resources and the number of pages and resources combined to figure out index ranking. With our new Merge Speed this should help tremendously.
With Merge Speed we look at your themes files and will automatically merge them into a single file. For example here is the popular Blogus theme which as many layers of CSS and JS causing bottle necks for mobile. You will need to scan your directories reorganize the files and then our software will take care of the rest, you can even theme over the original theme files in order to write custom CSS or JS that will work on top of your theme based on your own use case.
Merge speed should help you get your site from a 60% score into the 90 range. This was tested meticulously to be helpful. If you theme uses many sub folder you can define the sub folders under install options your can even reorder the files, and delete ones you are not using in the Resource dashboard.
We are releasing this feature today and will be available as a free upgrade to existing users.