I agree to some extent, but I don't think it was designed to look better rather than to be immediately reminiscent. Certainly the Giger designs are superior, more intricate and elaborate, but I assumed it was a deliberate attempt not only to make the Juggernaut look clean but to make it look like the derelict was a much more ancient vehicle, built (or grown) in a different way. Much as the urns are an advancement on the eggs.
I look at the Engineer tech to be a simpler cleaner aesthetic because that tends to be the way that tech changes, whilst I look at the aliens in Promethues as simpler or bigger because they haven't developed into the ultimate weapon due to their watered down (in plot terms) conception, and are therefore a deliberate deconstruction of Giger's alien.
It's either a legitimate reason for the simplification and smoothing of details or an excuse to give the designers a pass. A bit of both probably.