I think the key advantage for CO to have the 737-900 is they can sub it on routes scheduled for another 737 (300, 500, 700, 800), without messing up pilot scheduling.

I know that CO routinely swaps the 737 fleet around based on projected loads, and has a whole team of people that work on that exclusively. Example - I once flew EWR-SEA on a 737-800 although it was scheduled for a 737-700. Since this was not a day of departure swap and had been planned a week or two ahead of time, CO was able to fill the plane 100%.