Really good ideas!
- being rescued : This was in the game at one point. Your followers could revive you. It probably should be added back in.
- watch towers : I like this idea. Maybe have a siren that goes off or something
- special non craft-able items as rewards : This is planned
- special people joining your cause : I have a lot of neat unique followers planned
- diplomacy / requesting help : I've thought of some sort of rep system. Still trying to figure out how it would work
- turning into a cyborg : I am planning a suit (like a exo suit thing or something) that will give you science powers [no magic though]
- turning the start talking robot box thing into a walking talking robot box thing : As you get further in the game E.D.I.E. will get parts added to it (which is why you can't build right next to it). I haven't talked about the ending of the games story, but some of the things you mentioned might be in there.