The "broken by design" part is due to the fact that the pool pays by generation so payments are limited to the 50BTC, plus income from fees, that can be fit into that part of a block. So, since the PPS system means that the pool can reward more than 50BTC during a round, rewards accumulated during long rounds cause a backlog that will have to be fit into future blocks.
Once you get over the threshold, you can get an estimate on your place in the queue on this page made by twmz:
http://eligius.st/~twmz/And yes, I agree that it could be made a little bit clearer, since the information about the payout threshold on the stats pages dates back to the time when the pool was still proportional.
Nice explanation. If your tool generates a computer-readable dump somewhere on the disk, I could read it and show an estimate "you should be paid in X blocks" (and linking to your page of course) instead of the misleading explanation. But then again, it would be all the more upsetting because it's just an estimate. What do you think?