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Good point. I assume that miners will choose to mine the version of a transaction with the highest fee-per-kilobyte, since that will give them the best profit, but actually changing the code to implement that policy has been controversial when I've brought it up before.
To fight transaction spam, I think the relaying logic will need to get smarter, too. A large, expensive-to-verify double-spend should be way down on the "stuff that should be relayed when there is enough bandwidth" list.
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That's a different issue, and a new feature. I think the best way to implement that feature is "child pays for parent" (see https://github.com/bitcoin/bitcoin/pull/1647 for a proposed implementation), and then the user can broadcast a high-fee pay-to-self child transaction to get the parent accepted into a block.