EFI question

The only thing holley does that megasquirt doesn't do is closed loop WOT (including nitrous). Some argue it's a bad idea. Others swear by it, as it saved their motors in quarter mile passes when a fuel pump started to fail (multiple were boosted). MS3x stays open loop for WOT, and has AFR safety that you can enable and set the parameters- if the AFR's go outside of the window you set for that rpm, it will cut to a limp mode.

Fast, Holley, and MS3x all have very similar features. Factory computer has its own advantages, well really just one, being knock control (megasquirt has knock control as well, though I haven't decided to figure it out- it's not that simple)

My advice is this:
Use the system your tuner prefers. If you are going to tune it yourself, use megasquirt.

Footnote: I have a buddy who just swapped from FAST to MS3x on his 3G Hemi because he needed the diagnosing capabilities of MS3x. I'm sure he will sell the FAST. Rylispro on Moparts, maybe on here as well.