This is true that's why it's not really fare to compare. To me the megasquirt looks like a computer controled VPC and that's about it. It's kind of hard to compare the two when it comes to that stuff just because the aem ems is more advanced, has more research behind it, bigger user base and is capable of alot more.

http://www.megasquirt.info/index.html

Main link for megasquirt also.

After looking through the megasquirt sight somewhat it seems that the megasquirt doesn't even have a timing control unit. Plus the fact that it doesnt have knock control like the aem ems does for pussies like me. Also not sure how many ports it has for controling stuff like meth injection, nitrous(even dual stages) and so forth.