I am running into exactly this problem. I am looking at correlations between load and throughput. Literally (load,throughput) pairs. But if you are measuring a real system that is usually at load 1000, you may never get data for load in low values like load 1,2,3, etc. (ie: what is Google throughput at 1 user only? We will never get data for it.) So, what I want to do is to properly weigh all the data that I DO have. In the observed data, every observation has a weight, which is basically the number of times to include it in the MSE. I can't make up observations for "Google throughput at load 1", because that never happens.
It means that the equation for MSE needs proper weighting. If you think about it, this is generally the case for doing statistics! If you measure f(20)=100 1000x, but only measure f(5)=2.3 2x, and f(1) is never actually measured... So, in the rates. ie: say it's bytes/sec... keep separate byte and duration counts. You must weigh 2.3 byte/sec as 2 measurements if it happened twice.