This has been suggested before, in just a different form. Basically, give the captain the ability to "lock" crew slots as a certain role, so that you eliminate the 2 gunner, 2 pilot, ect. situations. I would still love to see something like that implemented.
That said, in my experiences, asking nicely nets the right result 99% of the time. If your boat is not ready, then don't ready up. Most players not willing to listen to you, also have low patience, and will leave. If you are more concerned about mid-game joins, either wait for a full boat in lobby, or pray. If you get that 2nd gunner, just tell him why you don't need one and ask him to change or politely leave.
In short, it would be nice, but I don't think it's on the priority list.