As far as your first brainstorming bullet point where I am right now is that the numpad (84562) controls the flap direction. 5 being a neutral up. 5 all of your thrust goes up, and the others are half in their direction and half up, so you still kind of fall and need some up flaps to stay aloft. This is pretty intuitive but has drawbacks for changing camera direction. I need to work on banking for that I think. I haven't quite settled on a banking mechanic for turning the bird yet (perhaps numpad 7 and 9) but I don't know how those should translate into animation that looks like something birds actually do, they don't really lead with their nose like a plane.
The second point you bring up is something I think I need to take really seriously. It is really nice because I already had already planned on using a feather texture that lacks an RBG color map and just using those channels to mask different feathers (I get my normal and roughness from displacement anyway). Point is for the feathers that are sexy plumage (the blue on a tree swallow) I could lerp between a muted blue and a bright one based on how healthy you are getting. I wouldn't have thought to do this if you hadn't mentioned it. I already want to track the players progress and use it to make the bird sing better based on how well you are doing.