I think it's too early to decide. After we see how AmigaOS4 and MorphOS compare, how the application support turns out, etc., then we would know if there's something to be gained from AOS on Pegasos. Ideally, I think it'd be neat.
Seems like Genesi wants to promote Pegasos as a multiboot board, so AOS would join the lineup of OSs for it. But as a practical matter it might not make that much difference if the apps are mostly already available on MorphOS and features are more or less equal.
-- gary_c