The paper "TCP Revisited: A Fresh Look at TCP in the wild", describes an approach to internet measurement which does scale to very large numbers of flows. This was my complaint about the first measurement paper we studied together, that it doesn't scale because it requires end-to-end measurements. This paper recognizes the need to make within-flow measurements and describes new algorithms for doing so, using statistical techniques. A few end-to-end measurements were made to validate the new algorithms.
Some might argue that end-to-end measurements are needed in order to get accurate results. While this is probably true, it may not be so true after looking at the big picture.
For example, let's suppose I can get very accurate measurements using end-to-end. Yet, because the measurements are end-to-end, the number of measurements is necessarily limited. If the number of measurements are limited, then we have less data with which to make inferences. It may be better to have a large number of less accurate measurements, than to have a small number of highly accurate measurements.