Hi and welcome on the forums!
First of all: EE 2.0 (although usable and stable) is still a work in progress and is still missing some features compared to 1.0 that will be added in the near future. You can check what, here:
http://www.esenthel.com/community/showth...p?tid=1507
1. I don't think it's a bad thing. You just end up with 2 folders: 1 for all your source assets (.fbx, .tga, .psd, .max, .blend, ...) When you import them (drag/drop), they get put in the project folder as an encrypted file. Which is fine because you don't need to touch them in Explorer again.
2. I haven't used any cloth or destructables so far. It's not in the 2.0 editor, but you can check the EE RPG 2 example for cloth on the main character (wizard). Both of those features are on the way, as you can see on the roadmap.
3. There are no .cpp or .h files in EE 2.0. They're merged into 1 "code" file (which I find really convenient, btw). The best way to find info, is to just open any code file, and press "ctrl + F", then just type in something like "destruct" and you'll find everything you need.
Just put it on "text in files" and enable search in "Engine" as well.
4. True. It took me a while to get used to the interface, and to be honest, I still prefer the one from 1.0 (sorry EE :( ). Now it just feels like a hovering GUI. But I think the asset management is pretty neat.
The F1 key does not work (it guides you to these forums) because previously, it would show the help file which is currently only for EE 1.0
5. I'm not sure what you mean.
As for the instantiation, you can just get that info from the Engine files (the green folder (library) named Esenthel Engine) + the tutorials project.
But I agree, 2.0 needs a bit more features. Personally, I'm fanatically looking forward to a shader editor.