Yep more sub layers would be very nice with the ability to carbon copy basic layout and affect elements in other layers for more intricate puzzle design. I loved making puzzle based levels and one of my favorite included between a past and present version of a level like in skyward sword.
Yeah puzzle design was frustratingly limited for me too. There are a lot of creative ways people got around certain limitations in the first game, but they were all insanely complicated and usually involved manipulating certain subtle mechanics or building complex contraptions offscreen. There's so much Nintendo could do to make this more complicated stuff easier, and since a lot of the part of the fanbase that made such levels were the most active and dedicated level designers, I hope they give us what we need.