Except that the longer you run the first stage, the longer you have to carry the weight of the first stage. It eventually becomes much more efficient to jettison the first stage and use a slightly less powerful but much lighter weight second stage, because you no longer need as much power to get through the atmosphere. Which is the whole point behind staging (
https://en.wikipedia.org/wiki/Multistage_rocket#Optimal_stag...).
It turns out when you add 10 lbs of weight to the first stage for reuse you lose approximately 1 lbs of weight from the max payload. (http://aviationweek.com/blog/nasa-cnes-warn-spacex-challenge...)
On the second stage every 1 lb of reuse you lose 1 lb of payload, which is one of the big reasons why second stage reuse isn't really feasible on the F9.