Parker is a bigger offensive threat than Rondo, and Duncan is still servicable in the paint. Those two advantages for the Spurs are also the two weaknesses that are killing us.
I think Ray/Paul vs. Jefferson/Ginobili is probably close enough to be, on average, either close enough of a wash to not make a difference, OR, perhaps the Spurs get better penetration (due to Ray essentially getting no penetration at all), which can perhaps also make for a more functional offense, but this isn't likely the cause of the huge difference in performance between the teams.
Our bench has been inconsistent, partly because our bench as spot-started so often. I think they've had more consistent production from their bench players, whoever they happened to be on any given night.
But my money is on the Parker/Duncan advantage, in terms of what skills they each have, or have left, as the case may be.