One thing I've noticed is that when you upgrade a soldier, they simply use up the new wares. So by the time an atlantean is fully trained, they've gone through five tridents, two shields, and two tabards. Obviously, they're not using all of those at once!
So, have you thought about them returning older equipment to the warehouse (for later soldiers) when a soldier upgrade? Or would that feel too unbalancing, even if you upgrade the costs of newer equipment to take that into account?
My initial reaction was to say that it's not so much that it would necessarily be imbalancing (especially after adjusting the costs of superior equipment), as that it would emphasize the wrong things. As SirVer in particular said, the emphasis in Widelands is very strongly on guiding an economy, not military tactics or even so much strategy.
But then I stepped back a bit and wondered why returning them to the economy would actually be a bad thing, and I actually don't think it would be. In fact, because it would also put a stronger emphasis on just how absurdly expensive a really advanced soldier is, it might improve the economic verisimilitude there too.
That said, it requires a fair amount of effort to change all that. Partly in the code to spit out the previously used weapon/armor (but not food) upon training, and partly too in the detailed rebalancing of all but the simplest weapons.
It's also possible that some weapons might require so many materials that their smithys can't hold enough to get started, and although the Atlantean heavy double trident and Empire war lance don't seem to have this problem, a naive summing-up of the Barbarian warrior's axe requires something like 9 coal, 3 gold, and 11 iron, while their war mills only hold 8/8/8 the same as the others.