Stock ECUs are good for mild modifications, but unless you can read assembly code, understand the logic and table locations in memory, you only have about 3/4 of the tables available to edit from opensource tuning. Ecutek and Cobb have in no doubt found more of the tables to edit. Add to this the relatively slow logging rate and not being able to tune in real time, it becomes a very time consuming task.
If going aftermarket I think the Vipec is the way to go if you want a lot of good features for the money. I have only been reading through the manual for the Vipec, but from what I've seen the closed loop fueling is really good, you can set up delays against RPM to account for the time the exhaust gas reaches the sensor.
The closed loop boost control looks pretty cool also, you can stage it so you run 100% WGDC up to say 80% of your target, then you switch to PD control until you get to say 95% of your target and then from there use PI control. I have been trying to replicate something like this in the stock
ECU, but I don't have the PD stage, just PI and it means I have to set the turbo dynamics a bit more conservatively to prevent spiking on gear changes.
It's just a pity the man behind Vipec Ray Hall has retired. But it looks like he has set up a good team to take his place.