I'm a HUGE fan of the HistWar concept. Basically a 1000x more strategic than TW is, and with more nuance and historical accuracy.
I have a good time playing TW, but I wish it had more strategic depth - delayed communications, scouting, army groups, etc. When I play TW the interface is intuitive enough that I can fully focus on what I'm doing in the game, which results in a more engaging and unobstructed enjoyment of the gameplay itself.
Basically, I want to feel comfortable enough with the interface that I can feel like I'm giving messages to my adjutants and not clicking around menus. I want to feel like I'm at my battle map making decisions on the fly.
Here's some ways I could imagine doing that:
First off, I would suggest making organizational schemes constant throughout 2d and 3d modes. Having different organizational schemes for different view modes requires that you learn something twice.
Maybe have a system of tabs to select the army group you want.
Click on a card once, and the units highlight on the 2d map or on the 3d map. Click twice and the 3d map will zoom to the unit using a convenient vantage point. In 2d mode this could zoom in on the unit. Right clicking on unit cards or the movement would then bring up the individual commands - attack, defend, attach, etc. Alternatively, there could be a context sensitive pane that displays orders in one static location. Then once a command is issued a dialog box could come up asking for any more detailed input required. Just a few ideas. Using two mouse clicks to center is much faster than clicking once to select, and then using a key to center.
This is a big thing - menus that you use frequently and contain the same info should be in the same place each time. It's simply mentally faster to go "Alright, this unit, I want to issue a command, mouse to bottom right of screen." The alternative is having the box pop up next to the unit on the map as it does now which requires one to always navigate to a new portion of the screen. It's just less streamlined.
I also mentioned some common computer commands which are always nice because they're the same in almost all applications. Ctrl click to select multipe, shift click to select a range, and right click to bring up contextual menus, etc. Why not use computer knowledge that people already possess? Same with viewing commands - ASDW keys are common in video games and are a better choice than the arrow keys because it leaves your right hand free to hit other keys on the keyboard. Also, most people use their mouse in their right hand, and so it's inconvenient to cross your left hand over to the right side of the keyboard to move the camera. Q and E then make nice keys for rotating the camera.
Hopefully this explains some of the concepts I'm thinking of when I mention TW games. Really though, I could use many games as an example. I just feel like I could be issuing the same orders with 1/6th the hassle.
And I can ensure without a doubt that if the interface can be cleaned up and professionalized a little bit there will be TW players joining the ranks. Making things pretty also helps, although even less important. With a little bit of texture work into the menus (I understand the 3d eyecandy will most likely remain very secondary) the game could look beautiful and also help one really immerse oneself into the gameplay. Things like nice backgrounds, no jagged edges, a pretty compass, a pretty clock, etc. This really isn't important to gameplay at all...but I do think a polished final product does help a player lose themself in the game a little bit more. A game is always better if you can recede from the real world for a little while, become fully involved in the experience, and really enjoy every aspect of it.