I think it just depends on the designer of the engine and his budget constraints. Not having a MAF sensor saves cost. Most motorcycle engines don't have MAF sensors on them, and the ECU's on most bikes are still extremely simple when compared to modern day automotive ECU's. Most autos also have two O2 sensors on them, one before and one after the CAT, but most bikes only have one 02 sensor, if they even have one at all. I think its all about cost. Motorcycle engines are still pretty basic in terms of electronic controls, though that is slowly starting to change. Motorcycle manufactures have never really felt a need to push the envelope on gas mileage numbers, and this is what has really driven auto manufactures to invest in better fuel control methods. However, there are quite a few cars running around now that don't have MAF sensors on them either, and just rely on speed density calculations and/or use static correction tables and alpha N.
I agree a MAF sensor makes (non-boosted) modifications much easier since changes to things that impact airflow will (for the most part) get automatically compensated for so you don't have to remap the fuel.
The up and coming method for modifying motorcycles is to download the ECU and modify the fuel tables in it and then reflash the ECU with the new values. This is starting to become more popular, and in my opinion it is a better way to go than adding a piggyback device like a Power Commander. Being able to reflash the ECU also enables you to adjust the ignition timing tables and other parameters (like secondary throttle plate maps, if so equipped, or speed and RPM limiters) and so it can open up a whole host of possibilities that a piggyback fuel controller can't do.