We have performed tests on SHA-256 and scrypt and have determined in all test cases that Prohashing yielded higher profitability than the comparable pool.  For example, SHA-256 profitability was about 104% of what Antpool was paying, even after fees from both pools.  Unfortunately, I don't have a Lyra2REv2 ASIC to test.

At Nicehash, we found that scrypt mining was paying 98.2% of Prohashing's earnings.