So... Wild idea.
Start the game mostly as you do today. But with 5 extra research points. Have a research group next to "Master" called "Field construction" where researched units can be researched again (same cost) to enable them for RTS production. For basic gameplay (no setting/story constraints) no field construction is researched initially. (You can spend your extra 5 points enabling troopers for RTS production.)
Now there's a significant cost to the RTS units (and a rather different premise for AI developers).
I think that's a bit too far out there. RTS battles are just far too dependent on being able to produce units for this to be much fun.
5 Research points is nothing at all, it's not a significant cost, and two, it's especially not a significant cost if you're just giving everyone an extra 5 points at the start that they didn't have before.
Everyone would immediately spend their free 5 points on that immediately. It doesn't help upping that cost to 20 points, it would just mean that everyone spends their first 4 turns saving up for that mandatory functionality instead of spending them on interesting things like unit or dragon upgrades.
As for building prices (strategy buildings): How about increasing the price of all buildings by X gold every time any building is constructed, and reducing the cost by X once at the beginning of each turn? (Never reduce below base price, of course.) That allows you to build one building a turn with no penalty.
The map gets full pretty quickly though, so that would be more interesting if there were ways to build more, or good reasons to get rid of buildings and replace them with others.
I'm not sure that the game really needed the last patch's increase to the building costs per number you own. The higher Campaign map unit costs already make you starved for gold. Adding hugely inflating building costs just makes producing buildings prohibitively expensive.
Uhm... I have loads of suggestions/ideas, some of which I think worth mentioning, but this (thread) doesn't seem like the place. Is there a place? Are suggestions worthwhile?
Of course suggestions are welcome. We may not all agree, but they're certainly welcome. You can make your own thread for suggestions and such.