I personally agree with many suggestions in this thread and my personal request is that the ship designer allows much more freedom in placing just about every object as it would allow for much more creative designs, sure it may introduce a lot of ahistoric designs but there is already mechanics like "weight offset" designed to nudge designs in a more historical direction.
A secondary request would be to allow us to change dimensions without increasing tonnage directly, if I could increase length and width but also make the keel shallower I think that could introduce an interesting design path.