I have experience with an RTEK and with megasquirt.
I built the megasquirt myself and have done some tuning with the help of others. It isn't the simplest to use for a beginner but it has a lot of great features once you learn it.
The RTEK is a modified stock ecu. You plug it in and you can start tuning, but it does not have all the features of a true standalone.
What plans do you have for your engine setup? What is wrong with the AFM or MAF as you call it?