Im an a1 owner but at the moment and since building and instaling debian i have not used it ,this is because i am waiting for os4.Which is why i would say only get an amigaone now if you dont mind using linux and waiting for os4 to be completed. As for the pegasos 2 it is now available and you have a 1 gig machine with a very nice amiga like operating software that has a lot of aplications ported to it already and is being updated all the time ,with the pegasos you can use it now. It is cheaper than the a1 and it is a very small form factor board so you can use small cases than the amigaone.
I hope to buy a pegasos 2 myself when i have the cash for it.. :-)