Definitely use Downtown Disney check in, we did last year and were so pleased we did. Our flight home was delayed by 5 hours which we wouldn't have know about till we had turned up at the airport. As it was we were delighted, a whole day more to enjoy ourselves. We just dumped the luggage with them, went back to the hotel, then had a fun day at Islands and Universal before turning up at the airport at 7 pm.
As the flight home then wasn't till 10.30 pm we had no problem resting on the plane because it was our night time and as a result we had NO jet lag for the first time ever. We were well chuffed.
I am hoping for another delay coming back this year.