Side-by-side and volume matched - I'd peg the M3 as sounding slightly warmer, and I think that is it's charm in a lot of ways. It has a quite nice organic sound. The X1 in comparison is just a little more spacious and possibly more resolving - but we are talking very small differences when volume matched.
Both sound really excellent with good IEMs and well recorded music.
The X1 has the more mature UI for now, has a line-out, and has roughly double the power output. It also supports gapless (the M3 doesn't), and plays more formats.
Yet in the last two weeks, it is the M3 I've grabbed when out and about - and isn't just new toy syndrome. The beauty of the M3 is its size and the SQ it has despite that. I've often just headed out the door with my U6 and M3, and it is quite liberating how tiny the combined package is. The M3 does have a shortage of features in comparison - but for those times when you need to be truly portable - it really is a wonderful little package.
And truth be told - as good as the X1 is, for the same footprint you really are better (IMO) spending a little more and grabbing the X3ii which I still think is the best value for money DAP on the market today.