Prototypes are the statues that are made by the masters at SSC in California. They have the best painters and costumers working on them. They make two prototype level designs, and then they send 1 over to china, along with the molds, and then the Chinesse factory workers have to try and replicate it. The problem usually is the paint apps and that is partially because the masters at SSC use completely different paints (including water color) than the factories do, not to mention the fact that the SSC masters are highly paid artist who get paid well for what they do, and who have a long time to get the work done, and the factory workers are underpaid and overworked. So sometimes the production and the protos can look very very different when it comes to quality.
However, there are other times where they get it damn close to perfect like Skarr, Gladiator Hulk, Superman,MJ, Gwen, and Punisher where they get the production pieces almost dead on with the prototypes. It appears to be a real crap shoot sometimes.