PCI-e is the way forward but there not going to leave everyone with AGP out in the cold. You can expect at least the next 2 generations of graphics cards to come out on AGP.
As for which shuttle to get, the SN85G4 is superb. Its socket 754 so to get the processor is really cheap. A 3400+ running at 2.4GHz (FX-53 speeds) costs around £120 now. Its a steal. The lack of a dual channel memory controller really does make no difference because its so efficient. There is no room for an upgrade but who cares. By the time the price of the new dual core athlon chips come down to a reasonable level there will be other new technologies and a new socket. My advice with a SFF PC is to get what you can at the time for the best value.