Honestly, for me personally, tech support isn't a concern. I know guys who specialize in both as well as guys who will remote tune them. Other than warranty issues or defects I don't really factor that in. Both systems are ~$1600 out of the box. So it's a draw there as well.
My hang up is that I'm a dummy lol. I relied heavily on the auto-tuning feature of the Holley to drive the 98 and just in what I've learned in the time since, I know just how much I left on the table. That doesn't scare me away but I know the MS3 system is a bit less user friendly for morons in terms of interface and the terminology used.
The "auto tune" feature is a cool selling point on both systems and will get your car technically mobile but every tuner I've talked to since has said "turn that sht off and fix your damn tune".