There's your answer: it makes no difference sonically, so your choice should be made on looks. If your wall is some non-offensive light color, in-walls will probably look better than "wall wart" speakers. If the wall is some custom color, or faux painted, inwall speakers can be painted to match. So it should definitely be inwalls.

Incidentally, as far as the terminology goes, since on-wall speakers sit some inches off the wall, it might be better to call them "bubos" (look this up AND read "The Naked Lunch") or "polyps" than "warts." That's it -- warts sit on the surface, but bubos and polyps have a stem of some sort.