Well, for one thing, the Axoloti isn't a 'finished' synth, you need to build your own front panel etc etc, which of course is one of the reasons people buy their Axoloti's, to build their own stuff, but when you want to pull up a machine that's got everything finished and ready to go obviously the Axoloti is not right.
Another thing I'd like to bring up is the difference between analog and digital (since you brought up the 0-coast for instance. I'm not talking about an 'analog sounds better than digital' discussion,, but rather the fact that when analog circuitry gets pushed to its limits, it tends to behave in a rather controlled way, whereas digital synthesizers tend to run into all sorts of digital artefacts which are usually less pleasing and harder to control, sometimes requiring knowledge of the underlying design and algorithms to figure out what's going on. Of course, that might be what you're looking for anyway, but I'd say there's a difference there when comparing digital and analog synthesizers, and it's much more noticeable in modular systems.
One such example is aliasing: when digital systems start generating frequencies above half the sampling frequency they get reflected back below that point, leading to often inharmonic overtones that only bear a fleeting resemblance to the actual pitches played. Digital oscillators such as the ones in the Axoloti (compare with the 'trivial' versions if you want to hear the difference; I think there's a patch in the demo section which illustrates this) therefore have anti aliasing features built in, and it works well, but when you start adding frequency modulation (FM), especially when you've got waveforms with lots of harmonics to start with, aliasing becomes hard to control effectively. On the other hand, when doing FM on an analog synthesizer you often hit the stumbling block that oscillator pitch stability becomes an issue, which is something that is never a problem in a digital system. Swings and merry-go-rounds I suppose, but the main point is that there is a difference (which may or not be important depending on what you're doing).