Well you can get a look at the Amiga One scecs for eyetech's site and the Peg II from pegasosppc site. As I see it. The Amiga One needs OS4 ASAP. The Peg with MOS has a huge head start. they are on the 2nd revision of the motherboard now. They have modern DDR ram where the Amiga One still uses olc PC100 ram, the Peg has firewire and can support much faster G4 processors so far while the Amiga one is running at a max of just over 800MHZ.
There has been talk that OS4 MAY get released for the Peg boards. I would say do it. It would give some much needed cash to the Amiga name and get thing flowing again. If you dont care about the Amiga name and are interested in an Amiga like OS on newer up to date hardware like you say, then the Pegasos II just may be worth looking at.
In any case its still to early to tell. None of the systems use the full potential of the boards with the current OS and processors. So they both will come out fast and very nice I would think.