Very true. I have been on several flights from SEA-MCO where a direct flight, stopping in MSP, earned fewer EQM than being on a flight making a connection in MSP, and then on to MCO.

I have been told that if I book a direct flight, say SEA-MCO, I get SEA-MCO miles, even though routed SEA-MSP-MCO. If I book a connecting flight SEA-MSP-MCO, I get SEA-MSP miles plus MSP-MCO miles. It is not a big difference, but if you are close to a status upgrade at end of year, it might be worth considering.

It seems crazy to me, especially if you have ever reached MSP and been told that the outbound segment of the direct flight leaves out of another gate. But I am told that is how the program works.