Based on what I have learned so far swapping in a Subaru EJ25, I would suggest going with an aftermarket setup (if you have the cash).
However, make sure to do your research. When you get an aftermarket ECU, it will come with a 'base map' (make sure it has one for your engine !) which will make the car run, but not run optimal.
To get the max out of the computer, you will need to get someone to tune it on a Dyny. Dyno time and labour for this are expensive.
The upside of using the stock ECU is cost. It is relatively cheap.
But make absolutely sure you get the ECU that came with your particular engine and also make sure you get the complete wiring harness !
The downside is wiring hell, and these ECU's use more sensors and crap than you'll ever dream off. If you want to do it right, and not have the ECU spew error codes at you then you have to make sure that all sensors are in place, or at least make the ECU think they are in place
Rob.