Ok bro, I've had the privilege of owning both units at one time or another. To be honest, it's quite hard to say which one is better. It all depends on how you want to use them. Do you intend to use the Nova System as an all-in-one unit in front of the amp, or do you intend to bypass the onboard distortion and OD and use it in the fx loop of your amp? Same question applies to the M9. What I can tell you that applies to both units: the distortions and ODs aren't fantastic. You're better off supplementing yr setup with your favorite dirt pedals.
One thing I like about the Nova System is that it has all yr basic effects blocks that you need: pitch shifting, modulations, delays and reverbs. And you can count on TC Electronics for their quality in these kind of effects. However, having said that...
The M9 is a wonderful tool as well. The various models that it takes after, though not 100% accurate, is still exceptional. You get all kinds of effects that range from ODs to reverbs. And the way it is designed, you can arrange them in any way you like and you can have repeats of the same kind of effect. Imagine putting three delay effects in one go! However, it's limitation is that you can only have 3 effects at any one time.
When it comes to setting it up and dialing in your favourite settings, the Nova System has bit of a steep learning curve. You've got to read the manual and practice before you can unlock its potential. But the M9 is much easier to control in that sense.
So there you have it...I guess it all boils down to how you intend to use them.
Just my two-cents worth.