Interesting, but why re invent the wheel? Rather then go into a HUGE mess of trying to tweak various things and leave it confusing for players, keep it simple and follow common standard.
Do the classic dungeon crawler color color coded rarity for these unit types. Grey, White, Green, Blue, Purple, Orange. As the game progresses have a formula or ratio of how units show up for the player side. Give a % bonus to stats based on rarity. That is the most basic form.
Of course you can expand upon this as you wish. AI Motherships and the Dyson Sphere are Orange. Golems can always be purple. The AI can unlock different rarities, too, all select able as options on the lobby.
You can further drill down, the skyis the limit. Ships can draw from a "pool" of attributes, with rarer types getting access to more total and rarer pools. Units that now have armor as a bonus can be called armored X. Ships that have extra HP are Tanky X. Your imagination again is the limit.
Keep it simple on the player end, and always ensure that it is presented as a bonus, not a requirement. Make it clear White ships are all that is necessary by having default AI behavior be white (naturally you can have an AI type that does not, all greens? All blues?)
