I'm not sure if there was similar suggestions already or not. Sorry if I repeat someone's ideas. What I propose is:
A. to give player's avatar (Hero) more active role in the game:
1. if he fights with his army, troops get motivation boost: stronger and high moral. (stronger attack and higher defense)
2. if he monitor production building the production increase as long as he's staying there.
B. I like this game very much, however I cannot help but wonder if it possible to add some female figures? I mean male workers is understandable, after all all of the manual work for settlers and serve in army require physical strength and other purely male traits. But it's a bit creepy for me to watch population growth without any woman present...
May be some women walking around residence, bakery, foresters, main house and some kids running around?
C. Food upkeep. No food => hunger => death of some population until there is enough food. I think it will give more realism to the game.
D. Bandits raids. Once player have army, perhaps bandits will attack him on random occasions? For food, women, weapon, etc purposes (If player fail to protect attacked building, bandits will loot some population (always population losses in case of player's defeat), food or other resources depending on building attacked.). Player will have to have troops to defend each sector. Or make them patrol all conquered area (troops do not stay at one point and constantly move from one building to another). Strength of bandits raids attacks will increase with each level player gain. Until player conquered whole island bandits attack from island. Once island is conquered there is no bandits left, pirates can find out about settler's base and start attacking for the same purposes as bandits.
E. Buildings:
1. herbs farm. (tool+herbs+wood+stone = healer house)
2. Healer house. (heal troops. Well, I don't think that every battle results in dead and alive only. There are also wounded. So healer can cure them. It's up to developers to decide if healer can revive some troops or just heal survived ones)
3. Cow, sheep, deer, fruit, vegetable etc farm. For food upkeep suggestion. Again, it's up to developers to decide which one or all of them.
4. Tower. for bandit raids suggestion. Troops can monitor area from towers, locate bandit raids earlier and move to intercept them.
5. Fort. For protection from pirate's raids. Perhaps even forming a fleet.
6. Church. Population growth => wedding Plus, having religious center is really important for stability of new settlement, granted there is no inquisition there ^^