Les is right, at this point it is still speculation, but I'd like to think about it optimistically in these terms.
An ECM contains two types of software. The first is the software that drives the Vehicle, the calibration software - it's all the parameters that you can't wait to get your hands on.
The second is the communication method between the vehicle and the diagnostic equipment - the communications with the outside world so to speak.
In this case, Cummins has changed the communications protocols with the outside world, switching from SCI to CAN.
I'd like to think that this change would have minimal impact on the calibration software, with the minor exception of as time has gone on regulatory requirements and technology has improved, which has driven parameter additions/changes.
I can say with some level of authority that the 2003 SCI ECM is very simplistic in comparison to the 2004.5 ECM. The 2003 is very 'basic' but how that transfers into tunability is yet to be seen. The 2004.5+ SCI ECM's are quite similar to their CAN counterparts.
Cheers
Cindy