I've got 3 huge designs:
1. A base design with psionic missles and minimal defenses, and two upgrade versions.
2. An intended upgrade to the first with better defenses and engines but the same weapons.
3. An intended design for new production, it has all the upgrades of the second, but uses cheaper photon torps for it's armament (same attack though).
Upgrading 1 to 2 costs 3300, upgrading 1 to 3 1900 despite 3 having 50% more changed parts!
Since upgrade cost is clearly not based on the obvious approach which would be to base it off of the cost of changed components, what is used to calculate upgrade costs?