We've actually had many of the same ideas you've suggested there; the fishing huts and the small house being upgradable into the larger house. The smaller house is, i think at the minute, more of an emergency worker supply for a tower- without spending the larger resource amount on the larger house => not having enough resources to build the tower you wanted originally. in the latest update we think we've improved the apple tree's overpowered-ness, by making it so the stockpile only auto-harvests farms; leaving trees to be manually harvested.
We definitely want to add different types of combat (footsoldiers) , other than the simple setup there is now- but the biggest problem i think we have is if we add 'too much' the game may become unnecessarily complex- which we think would ruin the simplicity the game has, which is one of its best features ( we think )
We really aren't sure yet- but right now, our 'storyline' setup would be more level based- with each level bringing in something new.
Thanks for the feedback :)