It would be nice but I don't expect that as generally the stock card is half length and low power and the 3870 is full length and needs additional power.
And I believe the reference design uses a 2-slot cooler. No room for 4 cards that way, meaning no 8 displays, and some people need that. Curiously, the 8800GT uses a single-slot fan as well. Which leads me to suspect the 4850 as being its replacement. It fits the bill, middle-to-high end card w/1 slot fan. Price is similar to 8800GTs pricing when the current machine was introduced.
I don't know about the stock card. 3650 is the direct successor, isn't it? The 2600 was a generation old even at release of the MP, so I don't see why they wouldn't do it again. The the 3650 is plenty for people not doing graphics work, and it can drive a 30in display. Why not? Well, it wouldn't be much of a performance boost, and maybe considering Apple's recent dealings with Nvidia, they may want to use another Nvidia part. That would probably wind up being the 9500GT.
For the high end...if they used a pro card, the Quadro FX 5800 makes sense. I can't see them NOT offering a high-end pro card, considering the MPs prominence as a creative professional's workstation. BTW, to whoever said the 8800GT and FX 5600 use the same core, they actually don't. The 8800 uses the G92, the FX 5600 uses the G80.
Their is another option. The X58 will allow for an SLI-capable Mac Pro for the first time. You MIGHT see an option for a second quadro, or possibly an Nvidia card in the mid tier as well (there is no single-slot card with equivalent power though. Maybe a 9800GTX+ or GTX 260, but they are both 2 slot.)