Gavin Andresen has an interesting blogpost about repackaging (specific) transactions into a new alternative blockchain for some tests that he is carrying out -
http://gavintech.blogspot.ie/2015/01/looking-before-scaling-up-leap.html. He is talking about it from a Bitcoin scalability perspective of course but I feel there is some benefit to looking at it from a Counterparty perspective. If it was deemed useful one could repackage all the Counterparty data into a dedicated Counterparty Blockchain. This would result in exclusive (no Bitcoin Blockchain) Counterparty Blockchain nodes.
Users could download Counterparty data from these exclusively Counterparty Nodes and even use SPV (Simple Payment Verification) with these nodes. If additional security was required of these exclusive nodes, Proof of Stake could be employed.
This way of looking at things considers The Counterparty Protocol not just as data embedded in the Bitcoin Blockchain, but as a raw unpackaged independent Blockchain embedded in the Bitcoin Blockchain. By packaging it correctly, native Blockchain features (like SPV for example) can be accessed by Counterparty users.
Is this idea viable or even good or am I missing something important (aside from the technical implementation!)?