1) You are double counting. There is no measurement of hashing speed, just an estimate. Stale shares (the end result of latency) are already not factored into the speed estimates.
I don't see the relevance here. It's not like I'm scoring the pools based on their estimated hash rate and deducting points for stales.
If anything, stales are just an indication of what I mean, just that I'm talking about a particular stale -> the winning share that became stale/invalid.
2) Your argument is circular. You have no knowledge about the distribution of hashing rates within the pools, but you assume that bigger pools have higher average speeds, and then you count that assumption as a confirmation.
Claiming every MHash is equal is also making assumptions, assumptions about each individual miner's network speed, each pool's network speed being equal. When working with large enough numbers, things tend to follow a similar distribution so usually assumptions are made. As long as the assumptions are reasonable and applied equally, then it's a valid basis until proven wrong.
Since this is a hypothesis, I wouldn't be surprised to be wrong in either the hypothesis or assumptions leading to it but you've got to at least put some data on the table to convince me otherwise you know
You are the one making the claim. The burden of proof is on you. I'm just poking holes in it, I have to prove nothing.
Let me try it another way. You are saying that 10 miners doing 500 Mhash/sec each are better than 100 miners doing 50 Mhash/sec each. As evidence in support of your hypothesis, you say that the big pools are getting more blocks than you would expect based purely on their (estimated) fraction of the (estimated) global hashing power.
The problem is that you don't have any idea on the composition of the miners inside the pools. Let me give you an example. BTC Guild is reporting about 2.3 THash/sec now, but it provides no data on the number or speed of the miners that make that number. Could be 9000 miners turning in ~260 Mhash/sec each, or it could be 15,000 miners doing ~150 Mhash/sec each. Could be anything, really.
So, you aren't actually providing any evidence to support your claim. Unless you have some reason to believe that the distribution of miners in the larger pools is unusual in some way, the whole topic of pools is an unrelated distraction.