1. Stay with a standard size for the motherboard... Unless, you're thinking of making some sort of drop-in replacements for Amiga cases. However, this would mean different form factors and cost increases. It might be best to just stick to standard ATX, or possibly MiniITX.

2. Whatever OS is more complete and stable. If possible, add compatibility to both.

3. It would be "neat", but I don't see much use of Zorro slots. There is not much hardware that aren't available in PCI format. The Video Toaster requires a video slot and the Amiga custom chipsets, so that's out of the question.
It might be best to look at a way to implement Zorro slots as a seperate expansion. (PCI Card?)
4. Would be nice to be able to use my CD32 joysticks...

I'm not sure about Amiga Mice, since I tend to be partial to optical mice now-a-days.
5. I'm using a PC adapter keyboard on my Amiga anyway. I would state that PS2 might be best. However if not available, then go with USB.

6. PC keyboard works for me. Perhaps bundle some stickers to relabel PC keyboards keys to Amiga equivalents.
7. Depends on cost. Is PowerVR3 that much more powerful?
8. The A4000T is quite big. I think it would be nice to be able to offer various solutions from full, mid towers down to something like a desktop computer. The problem with tower-setups is that monitors never seem to be high enough. With desktop machines with a monitor on top, the screen is generally a good height.

9. Price? That's a bit difficult to say. What is your target audience? What are the targetted specs?
10. I don't know about name. Are you planning on getting licensing for the name?
11. Iffy.
12. Dreamcast compatibility would be nice, especially with the homebrew development happening on the Dreamcast. Yet, I don't know how well that can work if you're going for PowerPC CPU? Using Dreamcast Joysticks would be neat, but many people complained about the DC JoyPads. (I tend to like them myself). I don't know how you can use the Analogue stick though? Would VMU's do anything?