So in 4X games if you're going to upgrade a unit to a design in a compatible series (may not apply here) it's a variation on something like going to a base with a barracks and then paying a lump of currency to turn your old unit into the new unit (with the same experience level as the old unit).
On the premise that Elemental may have an economic system where all the unit equipment is being produced as goods and then shipped to the city where units are being trained with it, the above model would be cheating! Instead I propose one of two (or both) ways to deal with this.
1) A unit enters a city with the necessary equipment for the upgrade and then instantly upgrades, taking a small experience penalty for being unfamiliar with the new gear (proportional perhaps to the gulf between the new and old gear equipped.)
2) A unit enters a city with the necessary equipment for the upgrade and then spends a few turns retraining to equip the new equipment with no experience penalty.
The option to do one or the other of these two would give some flexibility when the pressure is on, and the mechanic opens up exciting possibilities for conquest. Imagine that with your superior numbers of spearmen you have overwhelmed a small city on the edge of a kingdom with superior technology. In fact, you've also captured a warehouse full of magic swords they were going to use to raise an army against you, and now you can equip your spearmen with them, despite not being able to make the swords yourself. I imagine the spearmen picking up the swords and shouting "oh hooooo!" and then, you know, arms accidentally get cut off. This gives you the edge you need to make deeper incursions into the magic sword kingdom, capturing more of their equipment as you go (perhaps even some as loot in battle.)
This is more of a goal than anything and I realize it raises a lot of questions in other parts of the game.