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Some suggestions:

New mandatory update, that would cripple there botnet for a while.
And we can find out if the theory is correct.

Make some 'registration' for solo miners.
If you are solo mining you need to provide a identification token that can be validated. The identification token must be requested 'by hand' via the pool/block chain.
ie: preventing automatic setup, users need todo some steps in order to be able to mine the coin. This way legit users can solo mine but botnet are likely to stop since it's lots of manual labour.

Could be something like a hash that need to be requested via a webpage with a captcha on it so that it can't be automated. Or anything.
Or block all solo mining (if possible). But that would be the least favourite option.
(although I think that if you have a low power cpu there is no reason not to join the pool, and we can prevent users from running there pc without any reason. Since the users with low cpu are probably less experienced miners)

What do you guys think?
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