I've never had a problem with doing what the OP is alluding to. I always ask the GA in advance if they're anticipating a full flight, and if not, I ask if I can bring the car seat aboard (if it's Southwest and it's open seating) or if I can be reseated somewhere where there's two adjacent unoccupied seats.

One time, though, I was flying AA, and was on a completely full 777 except for one seat, which happened to be next to mine. They made me gate-check the car seat because they figured the flight would be full at the moment when we got on. Apparently there was a last-minute no-show. It was nice having the extra space with the lap child, but considering how much DD liked her car seat and how much better she slept in it at the time, it didn't make things on the flight that much easier.