I know it's a bit late to weigh in on this, but I found myself in the same quandary a year ago when I was putting my CNC machine together. I ended up settling on Mach4 for a couple of reasons:
1. Testing with the Mach4 demo proved that it could do everything I wanted it to and I saw it as the more "future proof" investment to make. I actually thought Mach4 responded to GUI interaction (ie Jogging button presses, stop etc...) better than Mach3 too, but i did not qualify that in any way.
2. Mach4 has more modern scripting available to the user. I'm not a huge fan of lua scripting, but I like it a whole lot more than VB.
I know I'm muddying the water here by going against the grain, but I'm happy with Mach4. My only complaint, as you pointed out in the original post, is that it is taking a long time for the community to develop things like ATC scripts for Mach4. But I think that will change as the user base increases.