1. Set certain behaviors to automatically attach to scene
[...]
Cons:
Possible cause of confusion
Likely will cause additional manual effort because of deactivation/reactivation
By the second cons, do you mean that you would need to deactivate every single behavior manually, because they wouldn't be appropriate e.g. for menu? If so, I just want to remind of the possible checkbox "Attach Mass Scene Behaviors" made for these quite exceptional scenes.
Although I think that the idea of attaching behaviors to folders rather than to single scenes appeals me the most, now that I think of it. It may be bureaucratic in a way, but I don't think it's exactly the bad thing; after all, having a habit or organizing scenes into folders isn't something bad, is it? O.o
After thinking about it a bit more (although I don't know how it would be technically complex), I think that you could attach already packed behaviors to scenes, anyway, for example to change some attributes.
Let's say that there would be behavior "Init Physics", which would set gravity and other things to proper values. There also would be folder "Ingame Levels" which would have behavior "Init Physics" attached to it with gravity value 5. Also, this folder would contain 3 more folders, like (*generating possible lands out of blue, please wait*) "Grassland", "Volcano" and "Space". First two wouldn't have any behaviors attached to them, because they're very default; Space, however, would have behavior "Init Physics" with gravity value of 1. Because this folder is more "specific" than "Ingame Levels" (since it's contained by it), gravity would be set to 1 rather than 5.
Also, there would be scene "Last Boss" which would take place on some mothership with artificial gravity, and because evil aliens are used to different gravity than us, gravity value for this level should be something like 10 or so. So, instead of wondering what should be done, creator would simply include behavior "Init Physics" with gravity value 10, and this would count, as it's the most specific behavior here.
(I suppose that programmers would associate this idea with inheritance and overriding virtual functions... well, I hope it wouldn't be too complicated to make, because it could save a lot of work for us O.o)
I think that it technically would be best to do with some window for folder behaviors, where you could attach them, and then all the scenes and lower folders would inherit these as well. Also, in the behaviors attaching screen, for scenes as well as folders, inherited behaviors should be shown as well, with darker font, perhaps (overridden behaviors would show as normally attached ones).
So yes, I support the idea with folders!
EDIT: Come on Hectate, own up - you put the idea into his mind didn't you?
Now whose mind do you have in mind... I mean, who do you meant? I'm still not sure if you're talking about Darkhog or me. Assuming from the "his" it should be Darkhog, but you could've been mistaken. >_<
Also, Hectate, apparently you have became the local Puppet Master here... oh my, I have a doll in my avatar! O.o