Be very interesting to read you impression and comparison between X1 and X3...
My main interest is in the sound. I make folder-playlists, and just play them from the Browser folders, so my comparisons between the X1 and X3 will ignore most of the features, since I rarely use them.
I loaded the exact same playlist into both the X1 and X3. The playlist has a mix of classic rock, electronica (mainly Paul Oakenfold remixes), traditional and modern jazz, various types of classical music (chamber, symphonic, contemporary etc) as well as modern country and some Indian sitar music.
I use Grado SR80s, which I find to sound very bright on the FiiOs, so bear that in mind. But I also love the sound, once I've tamed the brightness. So my listening settings may be unusual. On the X3, I usually have the Treble setting all the way down to -6 or -7, and the Bass up to +1.
On the X1, I immediately had to deal with the very bright sound. None of the canned Equalizer settings tamed it enough, so I made a custom setting that reduced the various higher frequency levels way down, with only the two lowest levels at the normal midpoint. I liked the sound I got. Actually it's quite similar to how my X3 sounded when I first got it, which I really liked. (It's not that different from the X3 FW3.0, for those who followed the X3 FW changes.) The sound is clear, but it has enough warmth for me to *feel* the music.
But I'm one of those listeners who hear differences with the various FW changes, and the latest X3 FWs (3.2x) are even more to my liking (as well as one of the earlier ones). I hear/feel more "natural depth" with the current X3 sound.
So basically, I prefer the X3 for acoustic music, especially classical chamber music. It sounds more natural. However, both the X1 and X3 sound very good (and similar) with amplified music (most popular music styles) as well as very electronic music.
Basically I plan to use the X1 when I'm on the go, and use the X3 at home, where I tend to listen to quieter music.
P.S. I prefer the scroll-wheel of the X1. I got used to it almost immediately. I still have to look at the X3 to remember what to buttons push, even after half a year.