This question comes up a lot. I thought I would give my take on it.
The SERT is a very feature full product. It allows for many more finer adjustments in many areas.
One advantage is the ability to change the ECM constants. This is particularly important when a major upgrade is done to the engine. For example, an engine build from a 103" to a 110" is going to require more fuel. Both the SERT and PCIII can give it more fuel but there is a ceiling to what can be given. This ceiling is determined by an engine constant. If the stock ECM has a 103" engine constant, the PCIII can only vary the fuel a percentage from the 103" engine constant, this many not be enough to adequately tune the 110" build. With the SERT the engine constant can be changed to 110" and this increases the entire adjustment range preventing it from maxing out like the PCIII could.
Another disadvantage with the PCIII is it is a "piggy back" device. This adds additional electronics to have problems. While it may be rare, the PCIII is not built with the same construction techniques (quality) as the stock ECM. In the event of a failure, many times simply removing the PCIII does not leave an adequately tuned ECM for running the engine.
The PCIII can be tuned with a dynojet using the tuning link software much more quickly than a SERT can be tuned. While this is true it would also depend on your definition of "Tuned". It has been my personal experience the tuning link software does not do an adequate job. Even if the "tune" is then touched up by a tuner, the results can be less than expected gas mileage and not optimal performance. We have a saying for this type of "tune", Fat, Retarded and Happy. This doesn't mean you won't end up with a "Fat, Retarded and Happy" tune if you use the SERT but if you have a good tuner using the SERT, you are less likely to.
Not all SERT tunes are created equal. Far too often the SERT is not understood and in the wrong hands will be no better than a canned map. This is more often seen at dealerships, IMO. A canned map and 3 dyno pulls does NOT make a SERT tune.
I may sound anti-PCIII but I am not really, I just have a preference for the SERT. What I have experienced is we can out tune a PCIII every time. It takes us longer with the SERT than the PCIII but the end results are always the same, better gas mileage, better performance and smoother running. With the PCIII it feels like our hands are tied.
As always, check with your tuner and see what they prefer since you ultimately are relying on them and if they are not comfortable with the SERT, the PCIII will be a better choice.