I never ever had an issue with Axe FX midi.
Oh, I'm sure you did. Like, you cannot simultaneously use Axe-Edit and, say, your MFC, right? Why? Because it can't handle multiple MIDI streams well at all. Or fast-coming MIDI commands.
Now, if your automation is very simple (i.e. you change scenes once in a while) and you aren't using any other controller simultaneously, you'll be fine.
However, I've had a ton of headache trying to make it change scenes AND (almost simultaneously) launch an LFO to control the sequencer AND start looper playback. Basically what I got was a very inconsistent result, different from time to time, unpredictably. It could fail to launch the LFO or start it later than needed, or what not.
Part of the problem is limitation of the MIDI protocol itself, I guess. Part of it is that Axe FX only handles one MIDI channel. Part of it, I think, is that MIDI has low priority.
You can also see limitations in the wishlist thread - like people asking for a VU meter in Axe-Edit.
Axe FX's MIDI implementation isn't all that great, and that's probably to hardware limitations, unfortunately, so I expect no big improvements until Axe FX III, if it ever comes out.
It would be even better if Fractal got rid of MIDI for Axe Edit at all, and made a control plugin using some protocol really utilizing the fast connection we have through USB.