Yes, denying filesystem access (well, raw filesystem access--Apple gives you access to the "Documents" directory, etc), may be offensive to some, but for me this falls under the category of "sure, it'd be nice if it did more, but I'm not gonna be mad about it." The TI-82 programmable calculator didn't allow me to reprogram my keys or to redefine the built-in math operations, but that didn't make me love that device any less.
The "originally written" requirement is different because it's not something that Apple could restrict by means other than by telling us, "you can't do that." It's kind of like saying, "Don't program in a functional style", or "Use a model view controller architecture." Uhm, excuse me? I'll decide that for myself, thank you very much!