[Scott65]

I've never tried to use a stock ecu, but I think probably the main difference is the freedom to choose how you want to tune the engine. You mentioned MAF, and with the aftermarket standalone stuff you can eliminate that if you choose and use speed density instead(or alpha n, blended alpha n and speed density or ITB for that matter). Traction control can be tailored to suit, or turned off, easily. There's nothing that's "locked", except the limits of hard coding on some units. My MS3 has open source code, so those with the computer skills (not me) can even change that.