I don't see how your machine is any different from an AmigaOne or Pegasos. They all have AGP and PCI, and USB, and SDRAM. The one exception is that their processors are about 1,000 times faster than the coldfire you've suggested.
Assuming you're implying an integrated graphics and audio chipset(where you've listed AAA+ custom chips, I assume you are well aware that AAA+ was never finished, and would be horribly out of date by todays standards), who out there is going to be able to compete with Nvidia, ATI, and Creative Labs for top of the line graphics and sound?
PC's ARE broken up into seperate cntrollers these days too! You have a completely seperate graphics controller, and a completely seperate audio controller, and a completely seperate bus controller, and a completely seperate memory controller (usually done as a northbridge and southbridge).
Operating systems are what determine the feel of modern computers. When people don't like Windows, they move to Mac, or Linux, or something else, but a Mac isn't really all that different from a PC these days when it comes to hardware, sure it's a closed platform so there's less variety, but the OS is what makes people move to it.
Amiga will have to do the same. If it can't compete as an OS, then there's no point, but a "custom based" machine is only going to provide a piece of hardware that will take another five years to come out due to all of the design work involved, and it will be overpriced and underpowered compared to current machines.
Also, there's absolutely no point in making a new "Amiga" keyboard if it's going to support USB. You might as well just buy an OEM USB keyboard, and have some different keycaps put on it for the Amiga keys.
The truth is, there's not really any difference between what you've described, and an AmigaOne with onboard video and audio, except yours has a much slower processor, would cost an extraordinarily large amount of money and time to develop, and wouldn't be able to compete with whatever modern graphics and audio cards were currently available when it debuted.
EDIT - Added...
What we would really need, is a whole new idea or paradigm for the hardware to work with. Something radical and different. The Amiga custom chipsets are not radical and different by todays standards. They are EXTREMELY efficient at what they do, but they are incredibly old news. The reason Amiga worked so well was because of it's very different (at the time) design.
If there is to be a new machine that grabs people like the Amiga did, it will once again have to have a new design concept, and not be part of this "Let's up the speed and throughput club."
Hardware isn't that important these days (as every Amigan should know), it's how that hardware is handled.
