That's probably going to happen, but when is a big question. The only reason you would need 2 - 16x slots is if you are going to go with dual video cards which is possible with PCIe. nVidia is working on that and indeed, their newest graphics cards have a connection for a bridge for just such situations (its on top of the card, looks just like the usual slot connector on the bottom). The 8x slots are currently being used for partial dual cards, with the second card sucking what it can from the 8x slot.
The primary control on the number and type of slots are the chipsets. PCIe is based on lanes. So a chipset has to have so many lanes to support a given set of slots. For a single 16x with two 1x, the chipset would have to have 18 lanes. For a single 16x with an 8x and a couple of 1x, it would have to have 26 lanes. Currently, I think the maximum out there is 32 lanes but that's changing rapidly. I know there's plans for 40 lane chipsets.
Once the chipsets with sufficient numbers of lanes are available, then the MB manufacturers can decide how to divvy them up into the various slots.
Right now, PCIe is so experimental, nobody has any idea of what its capable of. Theoretically, there's no limit on the number of lanes other what we put on it. My guess is it will probably max out at around 56 lanes. 2 - 16x, 1 - 8x, a couple 4x and a rash of 1x. There's a very good primer at ArsTechinica - http://arstechnica.com/paedia/p/pci-express/pcie-1.html
- that explains things much better than I could.
Right now, the selection is not all that good, but in three or four months, there should be a much larger selection available. This is going to blossom rapidly. Very rapidly. There's no telling what it could lead to. Think about what was originally touted for PCI 10-12 years ago then look at what's developed. There are PCI applications that nobody even dreamed about dreaming about them. PCIe will do the same thing.