I've given that some thought as well. I don't think I have the ability to intuition required to have the mechanics be fun enough to just fiddle with in a kerbal space program kind of way where you just kind of want to tinker with what you can do. I think it will need to be sort of a survival imperative. I put in a heart rate, (or breath rate I haven't decided) toggle that adjusts the speed you can flap (and ideally stamina/health drain). I set it so that at idle the drain is zero, but... you can't flap fast enough to actually fly... I like that a lot. So you try and fly but you can't get it unless you engage with the mechanic. I think choosing a swallow or a swift will help with that a lot. You have to be in flight to eat so... As of now I think survival simulator is probably the right scope. If I can get to the stage where there is a tutorial fledging level, a survival/attract a mate level and a raise a baby bird level that is a complete game, but might be beyond the time limit for a solo beginner like myself.  I think maybe food-health-song quality might be the way to go where you need to have built up enough strength to consistently sing a good song to get a mate as a player goal. 

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.

Sorry I won't be able to do a web build as all I know so far is UE and I guess they stopped doing web support some time ago. Makes me sad as well.