Esteemed Ladies and Gentlemen at Stardock,
First, thanks so very much for taking on this project. I like Sci-Fi TBS but Fantasy settings have so much more potential for me. MoM is great, but current technology allows for something truly special. You have quite a challenge ahead of you, and I trust that Stardock is up to it if anyone is.
Second, thanks for asking our input. I don't know where to start because I can see so little of the conceptual and thematic frame you're building on. Hopefully my understanding will improve and my suggestions as well 
Third, some preliminary input:
- Facilitated micromanagement. I.e. Micromanagement that "scales" well. 6 clicks to build a building in one city is fine, 6 for each of 100 cities is very discouraging. But don't go with a complicated "macromanagement" scheme where the player gives general directives that the AI follows. I'm not looking for AI control, I'm looking for tools that reduce the number of clicks and keypresses necessary for me to express my commands to the computer. Defining groups of cities, rules for the inclusion of new cities into groups, giving orders to each city in a group, etc. On the other side, ease of managing the information about my empire; robust screens with basic spreadsheet-like functionality; sort, filters for inclusion, filters for coloring, ctrl and shift clicking to select ad-hoc groups, issue build orders via right-click menu without changing screens, etc. It's hard to know what to suggest specifically, but I'll be happy to do interface mockups and whatnot as the information becomes available.
-- caveat: don't want to require players to use "the spreadsheets" if they don't want to
- Parties. Groups of Heroes. Beyond just stacking them in the same army. Group synergy bonuses, bonds of friendship, dungeon crawls (maybe), titanic smashing power. Is this in the scope of the project?
- Player Channelers as Heroes. Meaning they can move around and do much the same as a hero, be in a party. Huge tradeoffs in terms of ability to project power from the field vs. in the tower; vulnerability, concentration of force, etc. At all in scope?
- Multiple planes. Allows rich variety of environment, limited third dimension of maneuver, etc. An alternate plane could be slightly different and even startable (i.e. Myrror) or extremely different and so dangerous that only major armies need apply (e.g. an elemental plane for each element), etc. Any chance of this?
-- caveat: it's still got to be not-MoM, I suppose
- Keep end-user storytelling in mind. Highly embellished AARs (often novels in their own right) can be wonderful for generating a feeling of affection for a game. A robust set of "hooks" in the game really helps in the form of extremely detailed (optional) logs of pretty everything that happens. Having this dump into csv or some relatively easily processed format would be great, and some way of including "unseen" actions of the enemy (make it sandbox-mode-only or something for security or something) would be a nice bonus. I can provide more detail if this is anywhere near in-scope.
-- caveat: due to performance costs of logging, would need any non-trivial logging to be optional
-- caveat: logging actions normally out of sight of the player opens an exploit/balance can of worms, particularly if the game can be tricked into doing it in multiplayer
- Keep in-game storytelling in mind. In other words, immersion. Stirring, thematic music is critical here. Faces of characters are also critical; well done art, decent detail, large variation within race/class/etc. Dialog is critical. There have to be real characters, and they have to have faces, and they have to talk a lot
Probably don't want to go much into voice acting though, since that has to be done with VERY high production quality or it just detracts and is pretty expensive. Any of this stuff in scope?
-- caveat: a lot of players probably don't want characters, they want game pieces that don't chat back; so much of this would have to be optional. And "Options Are Bad", I know.
That's probably enough for now, I was trying to keep it short 
Thanks,
Keith