If you're measuring them as investors, you want the average, because if (as all these incubators do) they invest roughly the same amount in every startup, then average is money out divided by money in.
What is the average valuation of each class after the same time period? For example, the first class of YC vs. TS vs. SC vs. etc. after 1, 3 and 5 years?
This would show us the speed of growth of each accelerator compared to other accelerators when they were the same age. Even if YC has a higher average valuation now there might be an accelerator out there that has better valuation growth, but it is hidden because we are comparing baby apples to apples almost ready to harvest (sneaky apples to apples reference).
So yes average, but average comparing apples to apples.
Oooo... time for an apple :)