i've got the M9 and just got the Nova System like 2 days ago
nova system is used in the FX loop of an amp at home , the M9 has been a staple on my pedalboard for around 2 years now
They share some effects, but Nova system has a lot less (27 or so on the nova compared to 100+ on the M9), which it makes up for imo in tone quality, real pristine TC quality sounding effects
the M9 has a ridiculous amount of effects on tap which are also very helpful if you're prone to experimentation (e.g combing weird pitch effects with synth filters and reverbs/tremolos etc etc..)
the looper on the M9 is also fantastic, you can set up some effects, enter looper mode, lay down some kind of riff, put on say a bass octaver effect, and lay down a bass line within the looper , very nice
depending on whether you find one used or a newer one you'd be well advised to upgrade to the latest firmware or least v.2.0 before starting to setup banks/patches, the bass octaver comes with that, one of the effects i can hardly live without =0
the nova system takes more time to setup, and the parameters for the various effects seem to go a bit deeper and do to my ears sound better, the M9 is very very easy on the other hand, even the various effects have very straight forward parameters, easy to dial in
the M9 has 3 effects that can be activated at one time
the nova system has 5 (6 if you count the drive) but which are divided into mod, pitch, delay, reverb, compressor and drive
the boost function on the nova is very useful too
to be honest i was thinking of picking up a second M9, but a nova system popped up locally for a good price so i decided to give it a go, impressed so far
the drives on the m9 aren't too bad to be fair, haven't tried the nova system ones just yet, but i'd imagine they're better based on the other effects
some particular effects on the M9 that the nova system doesn't have:
octo verb (shimmery stuff ftw =0
particle verb
modulated delays/lo fi delays/sweep echo
various synth filters (q tron effects and what not)
looper
uni vibe
the m9 despite only 3 effects active at one time is mode modular, ie. you could have say the 6 available effects to be all variations of delay for example, as opposed to the specific ones on the nova system, although they can be linked up into presets/patches
hopefully that gives you some idea between the two