Nice analysis! I'm tempted to put a link to your post in the code as a comment...
The whole transaction prioritization scheme was written by Satoshi after I suggested that de-prioritizing "small new" transactions might help the spamming problem. In the last couple of days we've exchanged email about possibly modifying it; pull request 88 is the first suggested change (it makes the CreateTransaction fee calculations match the CreateBlock calculations).
Until somebody finishes implementing lightweight 'headers-only block download', we should try to keep block size small-- otherwise new users will have to wait an even longer time before being able to use bitcoin.
Also: the Faucet is now paying a 0.01 BTC fee per transaction. With the CreateTransaction fix, it probably would be anyway (the transactions it creates look very spammy).