I prefer the flat genericish cover with the other covers in the bottom thirdish.
To me, and this is purely opinion, I think the 3-D look is sort of gimmickish. And a tad bit misleading. Before you jump in and tell me why I'm wrong, hear me out, and know that I know I am outlier. In print a box set means a little cardboard box with an individual copy of each book. That's what I thought I was getting when I bought my first box set, 5 individual ebooks sold in a single package. Finding one massive book was annoying. Now, I'm not saying the author intended to mislead me with the 3D cover, but it did. I don't think that's a problem now as it was then, but ever since I've had a visceral distaste for 3D covers.