I read back up on merge mining, and actually since you can do fee-less blocks it's possible to do this in the existing Bitcoin protocol, but it's different from Merge mining in these ways;
1.) Merge mining does double mining, whereas what I'm describing all mining resources are directed at the Proof of Work blockchain. The cryptocurrency blocks are built at the same time as a Proof of Work block.
2.) There is no pretense of being a Bitcoin block, so a dedicated Proof of Work block would be more efficient. No transactional information or scripting would be included.
3.) Bitcoin would be only optionally supported by miners.
The main advantages I see with this system is that it allows arbitrary experimentation in cryptocurrency designs while retaining PoW infrastructure, it creates a marketplace for Proof of Work hashes so that transaction costs can be computed by the actions of the market participants, and it allows centralization of cryptocurrencies while retaining decentralized consensus of their state. The Proof of Work provider could also include other services like "smart property", not just cryptocurrencies.
This allows for experimentation but less than with an alt, because you are limited to the protocol that exists.
The only limitations that I'm aware of is that the cryptocurrency must be a Proof of Work cryptocurrency (Which is the only type of cryptocurrency that achieves decentralized consensus that I know of.) and the confirmation times would be longer. Are there other limitations?
Sidechains are more strictly limited by design. Merge mining, and this slight twist on it, are much more lenient.