Dunno Manu, i'm not sure how much of gnu/linux you could change, and still have it run all that software. Where are the Linux gurus? (yeah, Runequester you!) can the fundamentals of linux be changed that heavily? or would ir cease to be linux? or just an akward hybrid of the two?
There was a project that aimed to be an amiga like linux, was it anubis? not sure.
Anyway, you'd be better off altering BeOs/Haiku, as it's Amiga like to start with.
well, look at android, then look at KDE, then look at your wireless router. Linux is just a kernel, you can staple just about anything to it.
Changing the fundamental file system would be tricky, but honestly, I can't foresee that actually being a big deal. 99% of a users interactions is with stuff in his home folder, which is called whatever he wants it to be called.
A GUI that functions like amiga already exists, it just needs to be built out more and include a proper file browser etc.
Running native amiga apps can be done too, but it'd be a lot of work to recreate the api's. But it was done for WINE, it could be done for amiga too. Is it worth the effort compared to emulation? You tell me.
BeOS and Haiku are sweet, but then you are back at "limited range of hardware". Linux has it all, including stuff you wouldn't even imagine, and you get to tap into a lot of corporate support ensuring future hardware support as well.