We always put half my clothes in her suitcase and half of hers in mine, just for the reasons mentioned in the initial post. This is especially important when traveling overseas or when using a couple of different airlines.
Another thing to think about is taking a small suitcase with you on the plane. In there, put at least one change of clothes for each of you as well as your swimsuit. When you get to the pier, you could end up standing in line in a warm building and getting hot and sticky. When you get to your cabin, it'll be a while before your suitcases show up, so this way you can take a quick shower or freshen up and then put on clean clothes. This is especially helpful if you're flying in from a cold climate to a warm one. You've also got your swimsuit if you'd like to lay around by the pool.
Then, the last night of your cruise when you have to put your suitcases in the hallway, you've got your small suitcase to use the next morning for your nightclothes, toiletries, etc.
Instead of a suitcase, we use an expandable backpack that we expand for traveling, then retract for use when going into port for our towels, swimsuits, water, etc.