"Which is better in the longterm, Amiga One or a Pegasos board? "
IMO: Both are doomed to fail as mass product, but existance is anyway "good enough" for me. ;-)
Peg1 is a dead end (except that you'll be able to swap it to peg2 for 200€), and it is not anymore available (and for example HW drivers for peg2 will have priority over peg1 HW drivers).
A1XE is planned to have longer life than peg1, but peg2 has the potential to be faster, but only time will tell...
I would say AOS4 could have better future because it's not tied to any particular HW manufacturer ... but AOS4 does not yet exist and that is a very bad thing, as MOS is gaining momentum all the time while AOS4 stands still in the inexistance.
I think that when peg2 becomes available for Joe the Average, it would be very stupid to keep on waiting for AOS4 if AOS4 has not been released at that time.
I HOPE that after AOS4 is ready, it will be ported to several third party PPC platforms (Elbox, Matay+Sonnet, PowerMac, pegasos2), then it would have the best possibilities + the name.
The ultimate answer: A1XE is the best option today/next week, because you will be able to BUY it.