Protobuf vs. JSON was a deliberate decision. Afaik Protobuf was chosen
because of its strong types, less vulnerability to malleability and very
good platform support. Having coded both, I can say Protobuf is not more
difficult than JSON. (Actually the entire Bitcoin P2P protocol should be
based on Protobuf, but that's another story.)
Yes, all extensions to BIP70 should go into new BIPs. Note the plural
here: if you have orthogonal ideas I strongly suggest one BIP per idea
so they can be discussed and implemented (or rejected) separately.