We flew to Canada with a car seat for our 16-month old and flew back with the car seat checked in.
Pros and cons:
It is definitely safer to fly with the child in the car seat. That said, my LO hated being strapped in and I couldn't breastfeed her during take-off and landing. The seat in front of hers could not recline without her legs getting squished; tray table could not come down properly. When she is sleeping, I could also safely grab some shut-eye knowing that she is well strapped in.
When we found out that we could get two whole rows to ourselves on the way back, we decided to check in the car seat. My LO could lie down flat to sleep with seat belts strapping her in to keep her from rolling off. With this arrangement, though, it means that I couldn't really sleep very well, because I had to keep an eye to make sure that she wouldn't roll off (even with the seat belt on her). She felt "freer" with this option, though, and was a much happier toddler during this leg of the trip.
Sorry, not much help, as I still cannot make up my mind which option we'd take on our next trip. I'm leaning more towards taking the car seat if it's a full flight, but if there if we can get seats blocked off, then we might just check the car seat in.