The 3DS does not have the best wireless chip and downloading one game is already a serious pain the system. FreeShop can only download one game at a time due to hardware limitation and not software limitation. This is really not something that can nor should be overcome because it would render the system to a complete crawl.
You can download multiple CIAs, but you would also still be limited to the single filed batch installer through FBI. Basically the 3DS is not made to handle that much and it's a limitation we can't overcome.