The Skylanders Story's pretty much sum up as to how new Skylanders are appearing/chosen.
If a debate is over a S2 or S3, when you "bring the Skylanders back to life". There is nothing to prevent it from saying that they can't change upgrade "paths" which was a start from the get go, or "colors" which was also a start from the get go.
I think the most logical answer too this is that the Skylanders gained new powers by training in between the events of the games and the reposed toys are not canon.