I've been basically doing both at the same time this year. Up to this point in the year, there have only been three flights that gave me a higher PQM % than a PQS %, and it was only 1% or 2%. My next trip is TATL, so my PQM % will surpass my PQS % by quite a bit when Saturday credits, and it should stay there for the rest of the year. I'm going to hit Silver on miles and just miss on segments on the return flights (finishing the day at 29.5K PQM/29 PQS).
There have been a few times this year where I routed through a farther airport when it didn't affect the price of the flight (connecting through IAH or DEN instead of ORD or EWR), or taken a connecting flight (2500 PQM) instead of a direct flight (1750 PQM). I generally fly the day before I need to be somewhere (I really don't like early morning flights, especially since I live an hour from the airport, and the shuttle picks me up 3 hours before my flight), so the extra time doesn't generally cause an issue.