It's probably more accurate to say 'mencoder reflects the complexity of digital video' rather
then just saying the tool is complicated.
It's not easy stuff. There are a lot of choices you need to make between quality and
performance and trade-offs are a natural part of everything.
Linux tools like Mencoder or Transcoder are going to be what you need to get the best out of
your encodings. The best quality for the smallest files.. this is what their game is about.
Otherwise you have two choices... Either take generic defaults and sacrifice quality for
usability or have very large files and throw hardware/storage at the problem.
Cheap, Easy, Quality: Pick two.