Just look @ Stardock's previous game guys.
GalCiv2 allowed for full ship upgrading. I.e. you can upgrade from Constructor mk5 to a Colonizer Mk1 [Yes, going down, but sometimes you need it].
It didn't upset the balance of the game, instead it made obsolete units... useful, at a price of course.
The price IIRC, was the difference in default cost of the different parts of the unit. [I.e., ignore cost of similar parts, add cost of new parts)
So, yes, expect an upgrade cost to be 500 ish. But stardock knew many players won't be able to afford this outright, so they also implemented a "payment" system. You get to choose to pay outright, or a portion of it, then a weekly amount (with interest of course).
I see no reason not to implement this.
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As a side note, GalCiv2 had a problem where, when you unlocked the capital ship hull, there was no need to build tiny hull anymore because the of way the armor/weapon system work being subtractive rather than a ratio.
Since there is no such a thing as "hulls" for fallen enchantress, this wouldn't be an issue.
Although, this would make for an interesting development in fallen enchantress.
You can have 3 groups of "hulls".
1. The Mercenary [High cost, high Maintenance, low production time, 1.0 skill modifier]
2. The Conscript [Low cost, Low maintenance, Medium production time, 0.75 skill modifier]
3. The Professional [Medium cost, Medium Maintenance, Long production time, 1.0 skill modifier]
And that you can only upgrade troops from within the same "hull".
Just a thought guys, 