Allow us to choose what design to upgrade/refit to.

I second this. In fact when I played my first game and wanted to revisit my ship designs, I naively decided to destroy all my existing ship designs and recreate them again from a clean slate (perhaps with better names, etc.). It came as a shock when I realized that not only I couldn't upgrade my existing ships to any of these new designs, but on top of that I won't ever be able to upgrade them to anything since I've destroyed the original design.

At the very least the game should not allow the player to destroy a design "line" that is currently in use by any existing fleets, because no-one in their right mind would do that: how can you be sure that you will never ever want to potentially upgrade that ship before the end of the game?

I third this. There is a newer idea (somehow with more upvotes) asking for the same thing: Allow ships to be upgraded to any design of the same hull type. Those of us who want this implemented should upvote both ideas.