I actually like how resources are presented in Elemental. Food, for example, come in several varieties (Apiaries, Orchards, etc.), each which provides a slightly different bonus. I wouldn't mind seeing more of this concept. Take the Lost Library for example. Perhaps that also comes in several varieties (read: sizes). Perhaps you have an ancient forge nearby, which provides a lesser bonus than the Library does. Or perhaps you've found an old wizard's tower (smaller arcane bonus).
Having varying levels of different resources presents the opportunity for more resources to be spawned, and provides more drool factor when the big ones come up. Plus, it reduces the odds of the 'mega' resources all appearing next to each other, making those rare occasions when they do the subject of your next military campaign...
As for the 'refine resource x into good y' concept, that's fine if I'm playing Sid Meier's Railroads (Ore becomes Steel becomes Autos), but when I'm playing Elemental, I'm usually a LOT more focused on exploring, expanding, exploiting, and exterminating, so getting distracted with making cloth out of cotton is NOT what I'm looking for in the game experience.
Now, if I had to use 'x' number of the Crystals I just mined to build that Temple of Essence, that's a concept I can get on board with. Also, it'd be nice if we had a trade option that said "I'll trade you 'x' number of crystals each turn for 'x' number of metal". That way, having a surplus production has diplomatic potential. As it stands now, the AI is generally only interested in stuff it doesn't have on hand.
In short, making more interesting use of the resources we already have (as far as rarity and potential for trade) would be nice. I'd also like to be able to, as Kingdom, do SOMETHING with that Warg Pit or whatever it is. Sure, I can't use them for my troops (but my heroes buy Wargs instead of Horses anyways, 'cuz it looks cooler), but perhaps I could trade said Warg production for the horses the Empire isn't using...
Something I was briefly excited about when playing the campaign was those dark ore mines. Unfortunately, Relias wasn't allowed to mine these... Being able to mine different ores might have some potential for trade as well. Perhaps Ventri Metal is better than regular metal, with Ventri metal providing a higher % bonus to attack or defense strength. Or weapons made from Dark Ore have special traits... Dark Destroyer Blade has a nice ring to it!
While I'm on the subject of mounts, I'd like to see more of these, specifically Bear Mounts, Shrill Mounts, Slag Mounts... horses are 'boring' by comparison. This is high fantasy, after all!
Another idea would be to make Alchemists more interesting. You would provide an Alchemist with Crystals and Metal, and he makes you a supply of Elementium. You use said Elementium to make Elite Guardians that wear Elementium armor. Alchemists Shops might be a city improvement, or appear randomly on the map, perhaps as a resource or as free agents. He's the guy to talk to about Dark Destroyer Blades!
"Hi, I need a Dark Destroyer Blade"
"Excellent! I assume you have the required amounts of Crystal, Dark Ore, Shards, and Shrill blood?"