I see 4 options here.
#1 Stand alone EFI such as mega squirt.
#2 Piggy back the stock ECU. Again you could use MS and just have the MS control fuel and spark. This would leave the function of the check engine light as well as a few other things. But give you fuel control over the fuel and timing maps.
#3 Convert to Mass air. Tuning could be done by adding larger injectors and calibrated MAF sensor, a boost reference Fuel pressure regulator and locking the timing.
#4 Convert to Mass air and have a chip burned for it by a tuner.
Things you have to consider are your own level of knowledge. Using mega squirt is going to require you to have and intimate understanding of engines. You'll be creating your own fuel and timing maps, setting cold start enrichment among other things. But there is tons of support and information. So if you're willing to read and learn and do research then this may not be a problem for you.
Setting up the car using mass air won't leave as much work involved in tuning. You can hook a wide band and go make some WOT runs and tune it on the street/track. Or have a tuner burn a chip on the dyno which will result in better overall drivability as apposed to just locking the timing.
One thing you have to remember though is if you tune it yourself you better know what you are doing. Because stock parts + boost can = a pile of worthless junk quick.
I really like MS, and plan on using it on a project some day. It's true DIY and relatively inexpensive. But using factory Mass air has it's advantages in the fact that you're not starting from scratch, and the EEC-IV ECU is pretty adaptive.
Just my$.02
