I have a Peg1 but I think I can still respond to this question. I like my Pegasos and think it is the winner of your comparison by default (among other reasons) because of MorphOS. MorphOS has reached a reasonable level of functionality and has working games and apps and current development. MorphOS puts the "fun" in "functionality." Conversely the AmigaOne and OS4... I am not going to criticize it except to say that you see its proponents call OS4 "soon to be released" and so on. They've been saying this for three years but that aside, Pegasos wins by default.
Let OS4 be released and then we can compare again. Maybe then OS4 will be superduper "bulletproof" thoroughly betatested version its proponents claim. I have a more pessimistic view, but that's not my thing to criticize OS4. I wish them luck because its an alternative OS and sort of a "sister OS" to MorphOS. But no-one can argue with the fact that right now MorphOS makes Pegasos the best choice for Amigans, if you define Amigans as people who have historically used the Amiga 68K or PPC-accelerator-carded line of computers and who like to run Amiga programs.
If you define Amigans as people who support only Amiga Inc. and its partners and buy only computers branded with the Amiga trademark then I guess AmigaOne wins even though OS4 hasn't been released yet.
Now if you mean "I am not asking about MorphOS or OS4, I just asked whether the hardware of AmigaOne or Pegasos2 is better," that's another question. Pegasos is developed by bPlan, who have a long long history in the Amiga community and introduced the PPC accelerator cards and made the largest efforts of anybody to keep the platform alive in the middle and late nineties. So I find that that is a real plus that makes the Pegasos better for Amigans. Additionally I have seen the AmigaOne demonstrated and was not impressed at all. It ran a clunky version of Linux, didn't have any sound, and used UAE to run some Scala presentation and display large windowed grids of icons at slow speed. I am sorry if AmigaOne fans don't like me for saying this but it is true to what I saw and I am entitled to my opinion.
In its favor though I would say that AmigaOne benefits from having a bigger company MAI behind it. MAI is bigger than Genesi, so maybe they can put more money into AmigaOne development BUT this is is not evident yet from what I have seen. As far as I am concerned Pegasos is superior hardware and it is a nice small microATX form factor and the G3 version is very low wattage and saves you money on your power bill, whereas I recall reports (including one from Alan Redhouse of Amiga Inc. partner Eyetech) that people had to buy bigger fans because the AmigaOne was overheating.
Maybe I'll get screamed at, but that's my opinion and I think I have backed it up rationally: Pegasos is better.