Jetpack's Mobile Theme detection includes 2 filters, jetpack_mobile_template and jetpack_mobile_stylesheet, that allow you to define a custom Mobile Theme instead of the default Minileven:

Unfortunately, the custom theme still has to be located inside the Minileven module directory. It would be nice if you could use the filters to load a theme from the /themes directory, or from another plugin.

Reported here:
https://wordpress.org/support/topic/custom-mobile-theme-1