Currently a custom deployment is lost if you add anyone to a vessel, forcing you to recreate it entirely. This is a serious pain for what is otherwise an awesome feature - it means that, among other things, just having a soldier injured means you need to redo the entire custom deployment when you readd or replace them, every single time!
It would be extremely nice if custom deployments were retained instead - remembering the locations of anyone who died or was removed from the craft, and putting anyone else who is added in those locations. This might occasionally result in custom deployments getting shuffled or the like, but it'd be better than losing them entirely.
Another option would be to have each spot in the deployment assigned a number in the order of units in the craft. This would mean that losing or rearranging your soldiers could shuffle the deployment, but, again, I think it would be more useful.
A third option is to let users save custom deployments the same way we save loadouts... and to let users modify custom deployments from the embark screen immediately before a battle. Currently it seems like it's only possible to modify custom deployments in your base, which doesn't really make sense; the soldiers should be able to assume positions immediately before landing, allowing the user to choose from a list of their saved deployments right before battle depending on what they think they're going into. One advantage to this (especially if combined with the above) is that if the troops end up shuffled or in the wrong places, the user can just click to quickly check their deployment before battle and fix it.
EDIT: Someone else pointed out to me that you can make permanent ship-class-wide deployment layouts from the bootypedia view. This is much more useful, but is hard to discover. Perhaps tweak the interface to allow access to both the ship-specific and class-wide view from the ship menu somehow?
