I think a core question is, do we want mining to be human scalable or capital scalable.
Current coins including protoshares are capital scalable, you can mine as much as you can spend money. By requiring individual registration, or human-required interrupts like a rotating captcha you make it non-economical to run 3,000 servers if each server has an average 5 interrupts randomly per day. Doesn't matter if it's a cloud miner, doesn't matter if it's botnet, the human element does not scale like the hardware does.
To a certain extent this makes the guy with 40 computers in his garage the hardest working and best paid, requiring constant attention (5 interrupts x 40 divided by 24 hours in the day means an interrupt every 8.3 minutes).
I actually don't hate the idea of random interrupts, it incentivizes people run it on the computer they are actively working on because otherwise they'll be periodically checking at best or waiting for an email alert. One imagines a new suite of tools will emerge to try and automate this, and that becomes the arms race improving captchas.