Hi!
Well, whatever certain other people are saying,
the hardware of the two is more or less the same,
so it is more an OS-Choice than a hardware-choice.
If you want the official AmigaOS get the AmigaOne,
if you want MorphOS get the Pegasos (right now you wouldn't be able to get a Pegasos, though - Pegasos 1 is no longer in production, Pegasos 2 not yet available). To be fair I also have to admit that when
you buy an AmigaOne as an enduser NOW you will only get it with Linux and will get Amiga OS 4 for
AmigaOne shipped to you once it is available
for the enduser - should not take that much
longer though

.
It might be asides from a choice of OS also a choice
of company - I personally would put my faith more into Mai than into a small Amiga-market-originated
company like Genesi. Other people might prefer
Genesi for whatever reason.
For myselves, AmigaOne and OS 4 anytimes

I am sure I launched off a flamewar now

Steffen