I have reported these before, in multiple threads. Instead of bumping, I am creating this thread in which I will post a few issues which I have noticed while upgrading trained troops. I have never seen a developer post anything about upgrading troops, but I believe that this is one of the greatest mechanics in Fallen Enchantress.  So I would really appreciate having these issues addressed.

First a brief list:

[User Interface] When a existing custom design is being edited, the slots set to be automatically using the best available item are displayed wrong.

[Balance] Upgrade costs are hard to figure out, make little sense, and can be abused.

[Bug] When upgrading armor, items that were marked as 'do not upgrade' in the design tool still get upgraded.

And, at more length, with pictures

1. The design tool displays items improperly

Above I have created a design, the elusive infantry, that is meant to maximize dodge. The robes are supposed to remain fixed, because they provide a dodge bonus. The shield is supposed to be upgradable, because new shields provide a nicer bonus.

But once I revisit the design with [Edit] the tool displays both the robe and the shield as fixed picks. See below:

2. Upgrade costs do not make much sense.

Here I am trying to upgrade a different design, a leather wearing warrior.  There are 3 troopers in the unit, and every one of them requires four items, at a total cost of 14 loads of metal per soldier.  You would expect the cost in metal to be 42, and the cost in gold to be a multiple of the production cost of the items (they need to be made, and shipped to the unit)

Instead we are asked for 4 metal, which is 10% of the actual materials required to make the gear, and 183 Gildar, which is more than half the price of rushing the unit from scratch, and about twice times the cost of rushing just the gear being upgraded.

So we have two things that do not make sense. The metal costs are low, and the gold costs are high.

The first one can be exploited by producing a leather clad unit for no metal, and then upgrading it for 4 metal, saving 38 metal in the process.  You end up paying about 150 extra gold (the upgrade cost minus the production difference between chain and leather) for 38 metal which is one hell of a deal, most of the time. I've tried it, it works, as you can see below.

The second just makes it unnecessarily hard to upgrade units - it takes more to fully upgrade an unit (weapons + armor) that to rush a new one. 

By the way, I just noticed that the upgrade cost is the same for both the level 3 unit and the rushed unit, despite the level 3 unit's already upgraded shields.  Which leads me to think that the upgrade fee is independent of what actually needs to be upgraded.  Even worse.

3. Items that are not supposed to be upgraded are changed.

And now we come to the most serious one.  This one I call a bug, because it has the potential to ruin designs. Sometimes you do not want an item to be changed.  Maybe you have designed an unit for high dodge, and want to keep the monk's robe and cloak of shadows while upgrading to a better shield.  Maybe you have designed an unit for high initiative, and have done the math beforehand, so that by upgrading only a few pieces of the set you can get better armor without slow down.

Well, you cannot.  Remember the elusive warriors? If you upgrade them, not only do you pay an exorbitant amount of gold, but you also get the monk's robe replaced by an aegis robe.  To add insult to injury, you don't even get the much better available armors.  See for yourselves:

There are other weird things happening with upgrading troops, but I believe that by fixing what gets upgraded and what does not, the other issues will be resolved.

So, please, developers, the trained troops need love!  And aren't these ladies lovely?