I use the EmuMovies low resolution videos in mp4 and they work fine on the Pi 2 & 3. High resolution mp4 files have issues on a Pi. There are several threads about this.
I have the Pi 3 overclocked in everyway (CPU, GPU, RAM, SDCARD, etc.) and things are fine. If the .flv videos work for you that works too. It they stutter, maybe try the low resolution mp4 files.