I've installed and/or programmed several different after-market EFI systems. AEM, Holley Commander 950, Accel DFI, Performance Electronics, Megasquirt, ect. Now I'm starting to dable into my first OEM ecu the Mopar NGC-3. Let me tell you, mattsooty , dead on, there's no comparison between the aftermarkets and the OEM.
With that said, I'd have agree most with franzh acessment though. To paraphrase: OEM are unmatched in drivabilty,emissions, durability, ect. Most aftermarket systems can get you 95% of the way there with good programming, enough so that the end user barly notices any difference.
Although the aftermarket is at best only 95% of the oem, it will also be 95% better than the carburator it usually replaces.
To thruthefence; I've never cared for the Megasquirt and usually advise against it in favor of the ADDED VALUE of other aftermartket systems. It will "work" no doubt, but, imo far too much depends on the assembler and end user. I believe many first time efi users are enticed by the low purchase price, but imo its a bait and switch. You get no wiring, no enclosure, poor non-automotive spec headers, poorly placed board mounted MAP sensor, no other sensors included at all, little no vibe proctection, ect. Even most aftermarket ecu's go through some sort of validation testing for vibration, esd, thermal, ect,,, your MS unit is just a mystery. If you Add the value of all the NEW sensors, wire harnessing, ecu enclosure, and quality testing of any off the shelf aftermarket EFI systme INTO the price of a MS, it could be an EASY $1000-$1500 EXTRA!
Since a decent Accel DFI or Holley C-950 sytem is only $1000-$1500 brand new(usually including a new fuel pump too), the added value does NOT favor a MegaSquirt.