Which is better depends on what the architect/course owner is trying to accomplish.
--From a pure architecture perspective, function is by far the most important thing. Let the bunker take whatever form is most convenient to shape, construct and maintain.
--However, if the owner wants a course to "WOW" people, like say Shadow Creek, Wynn (Hmm..Fazio, maybe a trend??) then I think the form will take the greater weight. Of the Fazio courses I have played, many of them tend to have bunkers in 'un-strategic' places just to add fluff value to the design.
--So, IMO, if architecture and shot values and strategic merit is the main factor in design, then function is (and should be) the most important design feature in the bunker, but if look and style are the most important design feature of the course, Form will (not should, mind you) become the more important of the two.
--And I agree, a sand hole in the middle of a forest or on the side of the mountain won't look natural, no matter what you do.