Character Creation, stats and skills.
The main idea:
When designing units, be able to adjust the unit's individual stats up or down. This way you can have a unit with above average health, or above average strength without necessarily having to equip an item that augments their stats. Also with the tabs that read armor, equipment, and weapons add one more slot called skills. Have a list of skills you have researched that you can then train your units in.
In depth, how it would work:
Have every unit you create start at the same stat level, research and buildings could ultimatley effect what these stats are. So every unit you would create would have the same starting health, same starting movement, same strength, etc. As you spend points to increase the different stats it would not require more materials but rather more food, money, and time to train that unit. So players could have potentially powerful armies by investing time into training rather than materials into magical equipment.
Likewise if you lowered the starting stats, it would make the unit take less time, money, and food to produce; but you would have an inferior unit.
The cost of a trained unit could be based on not the number of a specific stat, but the total number of points invested in all the stats. So a unit with +1 in three different areas would cost as much and take as long as a unit trained +3 in one specific area. Also you could have the cost increase exponentially, so it would be hard to create super units outside of heroes.
Ontop of stats units could also be trained in skills, these would be special abilities or special bonuses. The more skills you train a unit in, again the longer and more money it would take to train. These available skills to teach a unit could also be expanded by research, thus adding even more strategy to the game.