After some times owning both the Micro and the m9xx, I would like to post some comparison between them. If you are interested in the Mojo, this should help too, as IME the Mojo sound almost identical to the m9xx. In fact, the m9xx can be said to be between the Mojo and the iDSD Micro, however it leans towards the Mojo more.
Overall:
I can easily see why a lot of people prefer the m9xx/Mojo to the iDSD Micro. They are simply more musical and more involving. The iDSD on the other hand is more neutral, no emphasis or no smoothing in any freq ranges.
Trebles:
The m9xx is much smoother. It gives the feeling that the trebles is sparkling without getting sibilant. The iDSD's trebles is cleaner and more energetic. For Heavy Metal I prefer the iDSD much more than the m9xx, but for Prog Rock that needs sparkles, the m9xx is definitely my favorite DAC.
Mids:
Once again "smoother" is what I'd use to describe the m9xx. There's no harshness to any of these 2, but the m9xx sounds a bit more laid back on some cans. The difference is not huge, though.
Bass:
More bass on the m9xx, even with iDSD's xBass on. Bass extension is better on the m9xx, though the iDSD is just fast and lean enough for Metal and Classical.
Soundstage:
There's no definite winner. On most songs the m9xx sound more spacious, but the iDSD's soundstage is just more natural and believable. Anyway the m9xx has better depths.
DAC:
I used both of these to feed my Little Dot I+ with Burson opamp (
did a review on this fantastic combo) and both didn't disappoint, obviously. I use the
iDSD more for Metal, Classical and Acoustic and the
m9xx for more laid-back music. I think the inherent traits of these 2 are better shown when they're used as DAC only, and they're both DACs that have an amp section (the m9xx don't even have a line-in for its amp).
Amp:
The amp sections in the m9xx and the iDSD doesn't add too much color to the sound, but most of the time I just use them as DAC.
While the m9xx can drive 2 headphones at once, the iDSD's amp wins hands down in my book. First of all, it has a line in to support other DAC. Second, the iDSD's amp is powerful enough to drive the HE6, which in my books is the 2nd-hardest-to-drive headphones of all time, just behind the K1000. I brought my iDSD to a meet and to everyone's amazement, it just beats practically every (big, cumbersome) desk amps present. In terms of power, of course.
In terms of functionality, the xBass on iDSD is useless. So useless that more than once I've seen people in this and other threads ask if their units are defective. The 3D effect (which is more or less crossfeed) doesn't sound too pleasant to me. The m9xx's crossfeed is much better. The Mojo doesn't have crossfeed in any form.
Buy & Sell
A lot of people I've spoken to sold the iDSD to keep the m9xx (or Mojo). Which also happened in my case. However, I don't take it as a sign that the m9xx is better, due to the fact that the m9xx and the iDSD are different (and both enjoyable) to me. That said, the difference, while enjoyable, is 10% at max, and again they're both solid choice. The reason I sold the iDSD is that my finances at the moment don't allow keeping both, but when iFi release newer generation for the iDSD I'd definitely buy it.
(I post this in both iDSD and m9xx's thread, so please don't be mad at me)