Seems to be very personal -

Wood Deck is wood, but of course it is too thick and once painted who can tell?

Metal Deck is scale thickness, but is so thin spacers are needed to install, and some have mentioned expansion/contraction of such a big piece of metal during summer/winter (the metal decks acn grow and shrink and move a bit compared to rest of model).

I've gone with wood becasue it fits nicely and I can have worn spots down to wood. As for the scale thickness, you realy can't tell becasue fo the darkness through the slats. I'm using metal hatch covers and putting cross-braces on them to show them open (the underside), and they give a real look. Actually, I ahve had to add plastic to the open hatches to double the thickness, I believe the metal PE deck is too sclae thin.

Hope this helps.