I have flown from NYC to MBJ a couple of times with a Miami layover. I HATE it! It isnt the airport....it's like you said, when you are accustomed to doing it in 3 hours and all of a sudden it's an all day thing.....well, lets just say I would have to be saving a lot more money to do it again!
For around that amount you can chg your flight from a layover to a direct flight!