How to remove unwanted 12 and 16 grid skin options?

This is actually a function of Fusion Accelerator but it's implementing a version of it in Fusion Core. If you look in the skins directory you will see a core.inc file which has the following code:

/**
 * Implements hook_fusion_apply_skin_PLUGIN_info().
 */
function fusion_core_fusion_apply_skin_core_info() {
 // Bunch of Skin Definitions here
}

So one could easily reimplement the function as THEMENAME_fusion_apply_skin_core_info() and do whatever overrides are necessary. See fusion_apply.api.php in the Fusion Accelerator module's fusion_apply submodule.

(Also moving this to that queue)

Great. Marking closed.