If the video files are incompatible with iPad mini, you cannot transfer them to the device using either of the above methods. Rather, you need to get them converted first. There are numerous video converters on the Internet that claim to be able to convert video files for playing on iPad mini. You can easily find one. When you get the iPad mini supported video files, you still need to transfer them to your device with or without iTunes.
A simple solution is download and install Video Converter App onto your iPad mini. This app lets you transfer movie files (both supported and unsupported) from your computer via Wi-Fi Upload or iTunes File Sharing. Then you can choose to convert them on the device directly. With hardware accelerate encoding engine, the conversion speed is acceptable. The converted video files are in iPad mini-compatible format. You can choose to play them on iPad mini, copy them to Photo Library, transfer them back to PC via Wi-Fi Transfer, and even open in other apps. If you have iMovie app installed onto your iPad mini, the good news is that you can open the converted movie files in iMovie for further editing and enhancing.