During my last game I did think of one thing that would add a new challenge. Eventually I had a stable ring of towers to guard my lands, and I never had to worry about anything on the inside. Occasionally a group of 2 or 3 pirate ships in the same spot might destroy a few tiles before the towers sank them, so the outer ring wasn't used for anything too important.
What I'm imagining is a way to keep the center of the island in some danger too, in the form of a different pirate ship type. Instead of firing its cannons, it could sit for some number of seconds doing nothing, and then fire a flaming catapult a random distance inland from the coast. Wherever the shot landed would be destroyed, or if you wanted to get fancy, have it animate burning for several seconds before finally vanishing. Something like this would have made my last game much harder.
You've probably already considered upgrade buildings, but those are usually an easy way to add some depth to a game, even if the upgrades themselves don't do much. Perhaps a bakery building that, when placed next to a windmill, causes all incoming food to be increased by 10%. Similar buildings could boost stone and lumber income. If you go this route I'd hope their bonuses wouldn't stack as you built more (that would become overpowered), and that they'd be quite expensive so that many players will flat-out never use them.
The "never use them" line probably seemed strange, but I don't think it helps as much if upgrade buildings are always going to be used. The auto-food collection building is an example of this, where I would imagine everyone buys it sooner or later. Manually collecting food after you've got a few mills going, is just too time consuming, and at a certain point that building is a necessity. That is perfectly fine, and I don't think it should be changed, but to bring depth it is good to have things people can completely opt out of using in order to develop differing strategies. The apple trees fall into this category. I've read that some people use them every time, and I've only used them once. We aren't all forced to play the same way.
The upgrade building idea is probably something you could throw in without much effort at all, but if you are interested in more complicated ideas I could suggest a few things:
Because towers are locked in a fixed position, defending gets tricky. This is good, but it also helps entice players into spending their hard-earned resources on a different way. Perhaps an expensive building (or a re-purpose to the current ship yard should you decide to change how a person "wins" this game) would let players dump resources in until a ship was created. This friendly ship could slowly circle the land and exchange cannon fire with pirates it runs in to. This would be an expensive way to guard against gaps in the tower defenses, until new land showed up allowing the gaps to be sealed.
The small house is something I've never used, but I hate to suggest removing it because other players may actually use them. If that house turns out to be unpopular with everyone else too, then it may be a good idea to re-purpose it. I can see the current larger house taking the place of the small one, and then a larger mansion/apartment/whatever being an expensive upgrade. Clicking on buildings and then choosing to upgrade works in many games, but I don't think it would work well in this one. The interface only makes us worry about clicking to collect resources, and I wouldn't want to see it cluttered up. It might be nicer to have the expensive super-house so that it can only be built on top of existing smaller houses in the same way you can only build a quarry on top of a stone tile. That approach to building upgrades would allow the interface to keep the same feel that it currently has.
My above suggestion about a bakery would be much better as a mill upgrade (placing bakery on top of the mill), but I didn't want to explain what I meant by that at the time.
Water/pond tiles could sometimes start with a tiny fish icon on it. A new building could be a little fishing boat sitting on the pond that collects food for a short while. Once depleted it would revert back to just the current water/pond tile.
Eh, I should stop rambling now, haha! Please don't take any of these ideas as "demands" or even requests... they are just ideas to maybe inspire you guys in some way.