If you are aiming for a Amiga clone with the feel of the classic Amigas you should do the following.
1. The board should fit in a standard ATX box with a ATX power supply I think. Otherwise do as you like!
(This is simply a way to keep the cost down)
2. AmigaOS 4.0
3. Zorro slots are not needed since there is cheap PCI cards available that do the job better. However if you find some odd custom hardware that there would still be an interrest to use, then maybe add one or two if there is space left.
4. Don't know what ZipStick is!
5. Go for USB! PS2 is on it's way out.
6. Keep the 96 key style, but don't neccesarily restrict it to 96 keys. Be prepared that there are quite many national key sets to take care of and that the US keyboards lack 2 keys.
7. Don't know PowerVR!
8. If you wan't to make cases I think it's a good idea to get inspired by the Commodore designs, since they afterall made all the classic Amigas. It would be cool if someone made a desktop modell like A3000D but with a DVD recorder instead of a secondary floppy.
9. Oh, that's the tough part. We wan't it all but preferably we don't want to pay.
10. If it's a true clone that would fit into the standard line, A5000 would be OK. That would ofcourse require an agreement with Amiga Inc.
11. Stay away from trademarks. OK for Amiga but drop NeXT.
12. It would be great to see a continuation of the classic Amiga line with the hardware of the future. Would be nice with custom chip emulation. Either hardware or software.
Good luck! ;-)