Please see my comment to the question. I cannot tell you for sure what to choose, not sure myself, but I can give your some words in favor or FFMpeg. I did not use Media Foundation, but I often heard the opinions that FFMpeg offers a much broader set of features compared to Media Foundation.
Please see some of my links in my past answers:
video (mp4) to Mp3 convert[
^],
how to convert image to video in C#[
^],
How to trim the video using Directshow!?[
^],
How can I allow mp4 files to play in my software[
^].
FFMpeg is highly universal, cross-platform, and it does not depend on 3rd-party products. Note that you can use FFMpeg (or libav) as just conversion utility, via starting a process, but you also can use one of the available .NET wrappers to use as a library; I provided some links in first 3 answers.
—SA