Kudos to the developers. Elemental had a (very) rough start, but it is really shaping up to be a good game. With that being said, here are some things that I would dearly love to see in the game.

• Make sure city is visible when it levels up. It usually is, but sometimes it is obsured by something. Alternately, you could put the city's current production of research and money on the pop up window.
• Make some way to point to a quest objective. When you first get a quest, it shows you the objective, but this is sometimes obscured by popups. Oblivion provided a button on the quest page that took you to a quest location on the map. This would help a lot.
• Show what shards you have in combat. This is a minor thing, but it would help to pick the most efficient spell.
• Give some way to let the player know that a city's has finished its last project and its queue is empty. Master of Magic, Master of Orion, and Age of Wonders all did this. It would really help managing cities.
• Provide trade goods, or something similar to build when a city is idle. Let the workers do something helpful. This could be a research option, like it is in Civilization, where you can basically build money, research, or culture. Here, you could build any of the resources or research. (Or at least money and research.)
• When a city resource is destroyed, have the message tell which city it occurred in, or post an event. Right now we have no way of knowing where this occurred, which is aggravating in a large empire.
• Give a warning when an hostile unit enters your territory. This could be toggled to no warning, warn only on enemy player units, or warn on all units.
• Give us a black market to trade resources. I hate having a game with buttloads of money but no metal. This would especially help with the rare resources.
• Provide a city overview screen with a list of cities and their stats (i.e. a table). Most strategy games do this.
• Provide a similar overview screen for heroes. This would help locate idle heroes stationed in cities.
• Provide a way to organize spells by level or school. (i.e. a sort feature, maybe with tabbed pages.)
• Give heroes extra hitpoints per level. With magic working now, the only thing that matters is who gets in the first shot. Up heroes HP so that they can survive the first spell attack and unleash one of their own (or close in and bonk them on the head). My suggestion is HP = 5 * (1+Level) * ConModifier, so a hero would have 10 hp at level 1, +5 per level, modified by CON.
• A toggle to not use magic in auto-resolved combat. I hate seeing my caster burn 5 mana to kill a level 1 monster when it could just go up and stomp it.

I will probably come up with a few more later, but these are the big ones right now for me.