I wanted to make my own version of HoMM myself one day, because I was really annoyed with the design flaws of the original and I doubt Van Caneghem will ever return to his games. But it is unlikely, that I will ever have a chance to make more than one game, so here is a proposition to improve the core rules of HoMM type games:
1. Limit army size by hero's leadership ability, like in the original King's Bounty. Each unit would have leadership cost. That will favor using several heroes, instead of a single strong one. Therefore larger tactical depth on the strategic map.
2. Limit max city's unit population by player's controlled land, like i.e. monster layers. That will force players to fight over map structure.
3. Allow splitting unit stacks during battle (in particular during the beginning of a battle), while maintaining fixed 7 unit type slots. That would simplify strategic map interaction by moving it to tactical phase, and greatly improve the tactical element itself.
4. Allow building map structures, like fortifications in bottlenecks, like mountain passes. That ability should be limited by facilities provided by nearby city or other structures, to have a way to disable it in some maps and encourage more strategic uses of such feature, instead of just cluttering whole map with fortifications.
5. Use Final Fantasy Tactics style turn scheduling system, where fast creatures get more turns, than slower ones, with hint for user what creatures will move in the next few turns.
6. Make unit upgrades auto apply to all hired units to avoid forcing player to wait until upgrade structure is ready. Upgrade system should be a nice gimmick, instead of a way to annoy player or force him to wait.
7. Damage to units (and heroes, in case HoMM4 style heroes participating in battle) carry over to the next battle, unless healed. To emphasize use of healing structures, abilities, items and magic. It also make armies with high tier creatures less unstopable. A mandatory requirement for 1. There are several obvious way to implement stack splitting with damaged creatures.
8. Unit stack specific items, like say banners, giving that stack some bonuses.
One can probably easily implement these changes into say fheroes2 engine.