I'd be interested in getting a new PPC system (as opposed to a PPC card for my old machine) and have noticed that there are currently two real choices: An AmigaOne/Lite or a Pegasos II.
Leaping into the frying pan, I'd say wait - wait for the AmigaOne Lite and OS4 to come out then decide.
PegasOS and AmigaOne are pretty much alike hardware wise, the real issues as I see it (future software support) have yet to manifest as OS4 is not yet ready.
MorphOS will run many *AmigaOS 3* applications. At such a point when AmigaOS 4+ applications become available, the situation becomes more uncertain. I have been considering this for months yet only recently have threads appeared discussing this aspect - which devolve into "licensing scheme" flame wars and such, thus avoiding answering the question itself.
It seems unlikely that AmigaOS 4 will be ported to PegasOS (another hot topic) and whether AmigaDE will is also a thorny subject. Thus, perhaps future applications will be split into either AmigaOS 4 native and MorphOS (QBox?) native, unless some agreement or solution is reached to run either on either, which as I said seems rather "nebulous" to say the least.
It may be that MorphOS native apps appear that will not be supported on AOS4 and that AOS4 apps will appear that will not be supported on MorphOS, or there may be solution which allows easy porting either way - who knows? It seems to me that if you want to buy NOW to run linux, MacOnLinux, etc. etc., either board will do. If you want MorphOS future apps go for a PegasOS, if you want to run AmigaOS future apps go for an AmigaOne. AmigaDE being a current hot potato I would say if you want to be assured of running AmigaDE go for an AmigaOne. Hence I say possibly best to wait a few more weeks and compare when the situation regarding furture support becomes clearer.