The daily limit of 660,000 transactions isn't an issue.  Payouts would only be done using one transaction per block, the coinbase transaction, which does not necessarily need to be limited to an arbitrary number of outputs.  The P2Pool payout logic described in the wiki is a little fuzzy, but I can see the payout being divided up between an equal number of outputs for the largest share holders and oldest (qualifying) share holders until the total award has been spent.  The only shares that would expire without compensation, would be those with a value less than a defined threshold or the limit of the monetary unit (less than 1 Satoshi).

To clarify my last post:

Satoshi wrote in his paper that "Nodes will always consider the longest chain to be the correct one..."  To expand on this, wouldn't it be fair to also say that whomever controls the longest chain has the power to impose a tax?

Even if we were to incorporate P2Pool style code directly into the client, we still won't have any way of proving that Alice is only running a single node and that her node wasn't being secretly controlled by Bob, or that Alice and Bob are not colluding towards some nefarious purpose.

I don't know the answer to this problem, or if it even is a problem.  Perhaps the 'central' nodes need to be operated in a completely open and transparent manner with positive identification of all parties involved with it's operation?