New Amiga could be like this:
What's the point if it runs Workbench just like any other hardware? Or do you expect such software to be hard-coded, thus preventing any forwards mobility?
AAA+ custom chips
To do what? Operate timers? Control floppy drives and IDE? Play sound? Today's PC chipsets are very much like what AGA used to be: hardware and bus controllers with integrated GFX and audio.
The only really nice thing about the Amiga was Exec, so a real-mode CPU crash gave you debug output, much like a protected-mode crash. Today's PC's still just lock up or explode randomly and you never know if it's bad software or an overclock problem. :-)
3D customable chip
Today's 3D chips already do just about eveything. A custom RAMDAC with a *proper* sprite engine would be nice, though. That would get rid of flicker for good if objects don't quite sync with frame buffer swaps. :-)
USB 2.0 as standard
Well, that's one thing the AmigaOne doesn't have. :-)
New 92 keys Amiga keyboard
It amazes me how few computers have dedicated undo/redo buttons. A method for overtyping would be nice, too, so you can use a keyboard like a typewriter. For example, why bring up a character mapper to find the (é) symbol, when you can just type (e), backspace, and then overtype the (e) with the appropriate inflection?
Still, most of that can be done in software using custom keys and remapping. You hardly need a custom keyboard so much as a "rebadged" keyboard.
Now its the time to think new.
PC's don't sell in the tens of thousands, anymore. They sell in the hundreds of millions. You have to believe that hardware standards evolved the way they did for a reason, even if Windows doesn't make much sense.
Of course, this is strictly in terms of hardware. For software, I don't think it makes any sense to make a brand new OS and then make it work just like Windows, UNIX, or whatever. If you're going through that much trouble, you might as well try to fix all the bad points and keep the good stuff.
It's easy to do that with software. Hardware is just a means to an end.