Your thought process regarding lower diffs for a miner has been argued to death over at MC, the consensus is no, diff does not have any long term effect on profitability or otherwise.
Anywho, I see a lot of posts whining about high rejects and swapping pools because of it. But no mention of profits had during said period. If you swapped away from a pool just because of rejects without considering your btc/mhs, you're stupid.
True that most people think it doesn't have long term effect. But IMO I think those conclusions are wrong, as pointed out in my description.
And again, I tallied the profit average between Wafflepool and CM (basically the same, CM 0.89% higher). However, CM has +10% reject rates (the pool average given at the stats page), and WP has ~<1% rejects (reported by many users, and I checked as well).
To do the math I'll use 3.33Mh/s for example
WP@ 3.33Mh/s --> 3.2967Mh/s after rejects
CM@ 3.33Mh/S --> 2.997Mh/s after rejects
Using average profitability from each pool
WP@0.010807 BTC/Mh/Day @3.2967Mh/s --> 0.035626BTC
CM@0.010903 BTC/Mh/Day @2.997Mh/s --> 0.032626BTC
Difference --> 0.00295 BTC
Not a completely negligible difference.