> The "magic" healing via the home base in exchange with money has to be turned off to make the effort of producing food reasonable.

Still not really convinced...
1. Healing is something you often need spontaneously - it getting bound to one of the potentially slowest production processes in the game seems like a bad fit.
2. Making it a scenario goal is just akin of bringing the old boring "produce X of stuff" back: There's no use for castles? Let's just make building them the goal of the scenario! That's just cheap.
3. Hunger mechanics are something we'll probably only bother with for the more hardcore settlement games, so having food just for that purpose still seems like putting it in a corner.

> According to the corn idea, introduce cotton. Cotton will provide the player with cloth (new construction material).

That's the idea I like best so far: Have it as a part of the higher-tier weapon production. Airships, grapple hooks, windmills (?) - all the stuff you want the player to not have access to immediately.

> Remove oil, cystal and sulphur

Uh, what? If that's seriously something Newton wants to push, he'll have to explain it better. Personally, he pretty much lost me completely at "oil is too easy to mine".