Yeah, this would be nice. It's not a huge thing, but its current implementation is much less efficient than it could be.
- Tool tips showing the + and - of each particular weapon/armor/item compared to the currently equipped item
It already shows that when you select an item in the store.
- Shops offer more unique items based on alliance, faction, technology, city location, resources within kingdom boundaries, trade treaties, etc.
- Cities can build shop upgrades
Unless I'm greatly mistaken, shop contents currently inherit directly from technology researched. This means difference according to faction and etc. will come along with faction differences in the tech tree. I don't think that you should be limited from technology that you've researched in any city, and I don't think having the capacity to upgrade shops would be able to bring anything meaningful to the table.
- Traveling merchants
It would be cool to see caravans have this functionality (though they, at least, could be somewhat limited in what they have). Random events such as "a merchant from the wilds has appeared, with a strange weapon he hopes to sell you" would be great though. In that case it should have a bit of its own interface, showing you the item, but still giving you the option to buy it, turn him away, redirect him to the private sector, (hopefully allowing it to appear in normal shops after some number of turns) or kill him and take it from his corpse. I don't see traveling merchants as an actual discrete unit on the overmap as something that would add much, though.