tCheapest way to deliver a payload is also central for science missions. More money is then available for the payload. Transportation costs are part of the mission budget. Also, with cheaper transportation, more mass can be carried as more science payload or cheaper spacecraft construction.If we're only interested in telecommunications satellites and ballistic missiles than the cheapest way to deliver a payload is central. But if the mission is supposed to be collecting data, it is obviously more complicated.
A lot of NASA's science (and science supporting) budget has to go into R&D and operations (i.e. actually running the missions so the scientists can do their thing).
Running missions is not that expensive compared to cost of spacecraft, instruments/experiments or launch vehicle.