Everything that has been define about the ecu... Has that been released to the public like the open port project and ecu flash? All I know of is ecutune, and there information regarding the svx ecu is a company secret.
I was going to go with MSII but MSIII has a freescale microcontroller dual core 16bit, build in usb support and an sd slot for data logging. I used a usb to serial converter when using my innovate wideband and ecuflash. I just did not like the quality of fit. It just sort of hung there.. too heavy in my opinion. So to keep it simple I opted for the built in usb. At $100 dollars more than MSII I would go with the simulator and the MSIII. Together they cost me $437 shipped.
As for ignition I myself am going to used the ford edis-6 module, and a coil pack from a taurus in a wasted spark setup. When I bought my engine the coils did not come with it. And at $50 dollars a piece, nope... not when I can get the taurus coil pack for $30.
MSIII has many additional features that I can't mention at the moment and will probably never use, but it is nice to know that they are there.