So do people think that SAM will (eventually) go straight to PCI-Express and skip AGP?
Absolutely. You can get SOC (System On Chip) PowerPC processors with PCI-Express coming directly out of them. 8641, 8640, 8610, 440spe, and the 460gtx even has gen2 PCI-Express for double the bandwidth per lane. There's more than this small list too. Stick one of them ports to a x16 slot and plug in your graphics card. (These CPUs don' thave a full x16 PCI-Express port, graphics cards are generally x16 connections, but you can run just about any card from any port size, such as a x16 graphics card off a x1, or a x4, x8, etc. The x16 slot may not be fully connected, but electrically it's compatible and physically fits, so all is good, just does not give full bandwidth the graphics chip is capable of) And vice-versa, a x1 card will work in any larger PCI-Express slot, as will x4 and x8 work in slots larger than they are themselves. PCI-Express is popular because it's for more than just graphics cards.
To add an AGP slot, you either do the PCI bus in an AGP slot trick like Efika's adaptor (and I do not think that just any AGP card works properly due to voltage differences in newer AGP cards), or you make up some AGP/PCI bridge logic in an FPGA since that doesn't seem to be an off-the-shelf chip these days and run your AGP graphics card on a PCI bus anyway. From a motherboard perspective, if it's electrically PCI, might as well let the higher-volume customers put a standard PCI card in it... There's very little demand for AGP in the high-volume PowerPC market today, and nothing other than graphics used the AGP slot to broaden its appeal.
All works out that you're far far far more likely to see a PCI-Express graphics slot (even if not fully x16 bandwidth in the electronics) for future PowerPC motherboards than you are an AGP slot.
Also, am I correct in thinking that you cannot plug an AGP card in a PCI slot?
Correct. They're physically different and run at different voltages and have some different pinouts. Like putting a square peg into a round hole. They made it different to help prevent less advanced users from putting it in the wrong slot and breaking something.