The automatic formatting of LilyPond is much better. The workflow is similar to TeX: you write content in a text format and mark it up, and the software takes care of the rest. The quality LilyPond can achieve is very good. With MuseScore, though the visual interface is more comfortable for many and has a smaller learning curve, there's far too much manual adjustment necessary in scores of reasonable complexity, and usually has to be done again when a piece is modified. It's possible to get the best of both though, by importing a MuseScore into Denemo, which uses LilyPond for typesetting. Some examples here show the difference, compared to using MuseScore alone.
I'm glad that it sounds like there is a way using denemo to go from MuseScore to LilyPond. Is there a way to go the other direction? Having the scores in a format with easy portability and long term viability seems very important.