This one's a bit of a mix of bug and suggestion, interface and gameplay, so I didn't bother to assign it a category.

First of all, I designed some units in the unit designer, gave one of them a dagger and a cloak. I played a bit, quit the game. I started up a new game, and when I researched Equipment, the unit with the dagger and cloak appeared in my unit list. Except, since I hadn't yet researched Melee Weapons, it didn't actually have a dagger. In fact it had no weapon at all, which I didn't think is even possible. I checked the unit's file in the My Documents folder, and it didn't have any weapon there either, even though it had had a dagger during the game in which I'd designed it.

Secondly, if you're going to have unit designs persist from one game to the next, give us an option at the start of the game to not use saved designs for that game. Better yet, make it like Space Empires IV, and give us an option when designing our civ as to whether or not unit designs will be saved for that civ at all. Obviously, unit designs will have to persist within a given playthrough, so they'll have to be "saved" in some sense. But in any case, the ability to turn off persistent unit designs across different playthroughs is important. After all, if I spend a few games experimenting with different unit designs, when I start playing for real I don't want to get spammed with a dozen new units in my training window every time I research a new tech.

Thirdly, if you're giving us the ability to create and save persistent unit designs from within the game, give us the ability to permanently delete them from within the game too. And yes, this one is just a laziness thing. Sure, I could go hunting through different folders to find the relevant files and delete them, but why bother when a single delete button in-game would make things much simpler?

Lastly, and I'm guessing this one's probably been reported before, if you retire a unit design, the unit will un-retire itself next time you load that save game. But given the general issues with save/load at the moment, I'm guessing you'll get to that one in due time anyway.