Actually the small size of the Wii, and now seeing those doors on the side/top for the extra ports is a good reason not to buy one. People with high-end home theaters typically have an equipment rack for all their gear (may be an actual rack, or maybe just adjustable shelves, but a vertical stack of equipment either way). I don't care if you want to say that people stack it vertically because all of the components are wide and flat, or that everything is wide/flat because people stack it - it still comes back to the fact that typically people end up with these stacks.
How does the Wii fit into that? It doesn't. If you lay it flat, either the slot-load drive has to be pointed into the side of the rack and be unaccesable, or both those little doors with the ports behind have to be pointed into the side and be unaccesable. When laying flat, only 1 side (the front) should have any type of ports/slots/buttons/etc. on it, as the other 3 sides are likely hidden/covered. The exception would be the back-side for your output cables, as most people want those hidden.
I don't know why consoles lately have all been supporting this vertical-stand idea, but it does not mesh at all with every other home theater component on the market.