We struggled with this same debate before our trip last September with our then almost three year old. We too were taking ME so we wouldn't need the seat while we were there, but still had to decide what to do on the plane. Our carseats we already had were too big to be suitable for the plane, so we purchased a carseat specifically for flying (used on craigslist). It's a Radian 80 by Sunshine Kids (new name Diono). The seat folds up and it is narrow enough to fit in the width of the airplane seat so you can still use the arm rests and it sits low enough so she could still use the tray table. Carrying it through the airport and stuff was really easy since it has a shoulder strap and carrys like a medium size bag, then opens up and sets up quickly once we got on the plane.
We definitely reccomend this carseat for flying with a toddler. It kept her nicely contained on the plane, since she is used to riding in her carseat. She rode great for her first ever plane flights. In comparison, she was more active and wanted to move around on the ME bus, which made us even more glad we didn't have those same problems with her strapped in on the plane.
Finally, we got some piece of mind out of having a seat with us in case something unexpected happened and we had to ride in a car. While it isn't really likely, we were more comfortable knowing we could rent a car or get a taxi and have a seat to put her in.