Alrighty, I started just outlining where I thought a game timer could go but man did it snowball. 2 hours later it's turned it into a whole mockup and detailed breakdown.
1.(Dark purple) If the top left is unused, then the rally flags would be better else where. Age of empires 3 sets them top left, while Starcraft 2 sets them in the bottom center.
2. (Cyan) As others have mentioned this should be shrinkable. For campaign mode it's important that players see their objectives as they will probably vary while in multiplayer it's almost always going to be static. Changing it to be a player info screen also makes sense in multiplayer.
3. (Orange) I think the veins of evil or any other screen taking up most of the play area should be partly transparent. Seeing your dungeon in the background would give the feel of a staying in the game rather then navigating to a research page.
4. (Red) An in game timer showing the current match time. Almost every RTS game has this and is useful for timing attacks in multiplayer
5. (Light Purple) Spells are often split second game changers. Control group rally flags will probably be hot-keyed to 1,2,3,etc. so having the letter keys map to spells makes sense. Using Shit + (letter) avoids accidentally moving units it and holding shift could bring up a small menu reminding the player which letter selects each spell.
6(Yellow) This is the most important change for me. The minimap should be twice as large as well as the buttons and into panels. I've added a screenshot from SC2 for comparison. Look how their panels take up around 2/5ths of the screen compared to WFTO taking up about 1/5th. Checking other games like Company of Heroes or Age of Empires shows the same ratios and for good reason. Try to quickly move your mouse from the center of the game to a button and you'll notice how easy it is misclick if you try to go fast. The same for the minimap, the larger it is, the quicker you can zoom around your dungeon.
7(Black) Most RTS games have a ping button on the minimap, The library button could be added to the menu or moved over next to the objectives.
8(no color). Just to make the game more aesthetically pleasing I think it would be cool to add some decorative border to the UI. Things like chains,skulls and stone like the way the SC2 UI has tentacle looking borders for the zerg player. Of course the WFTO mockup wouldn't have shown this but I thought I'd mention it anyway. .
9.(no color) This last one is not really UI but a quick pickup/drop with the alt key would greatly add to player control. Individually picking up units takes quite some time. This could be fixed If I were able to hold the alt key then drag the mouse over several units. Each one that I touch while holding alt will send it into my hand. Dropping a unit while holding alt releases all held units. Pressing Alt + (control group number) would send that control group into my hand. If the control group is too large it would fail and give a not enough mana warning.