Hi Darrel,
The biggest advantage to certificating the aircraft as amateur-built would be that you would NOT have to conform to Van's strict assembly instructions when building the aircraft. You could use a different prop, different engine, different instruments/avionics, etc. if you like. You could even equip the aircraft outside of the LSA definition if you wanted (although it would then be forever ineligible for operation by sport pilots.)
Another advantage is that, assuming that you perform the majority of the building (and assuming that the aircraft meets the major portion requirements for amateur-built certification, see below) you can get the repairman certificate without having to take the 16 hour LSA repairman course.
Now the other side of the coin;
1) You would have to be able to prove that the aircraft meets the major portion requirement (aka, the "51% rule") for amateur-built certification. Van's has not (to my knowledge) issued any sort of guarantee that the RV-12 meets the requirements for amateur-built certification, and it has not been evaluated by the FAA. This being the case, it's up to YOU as the applicant to be able to prove that the aircraft does indeed meet the requirements for the amateur-built certificate.
We should see the new guidance regarding amateur-built certification (including a new 8000-38 checklist) from the FAA any day now. The RV-12 will have to meet the new certification guidance, so we'll know more about this issue in the near future.
2) Your name is on the paperwork as the "builder" if you to amateur-built. If you go ELSA kit built, Van's is the manufacturer. Some people see this as an issue and some do not. Just wanted to point out the difference.
In either case, once the airworthiness certificate is issued you are free to modify the aircraft as you see fit, although in the case of ELSA certification you need to keep the aircraft within the LSA definition. In the case of amateur-built certification your modifications could carry the aircraft outside the LSA definition if sport pilot operations are not an issue for you.
Hope this helps!
Joe