1. An all-Intel system is most likely going to cost more than an all-AMD system and offer fewer features, but it is also quite a bit more flexible and easier to work with from a software standpoint. Intel's IGPs support XVideo Motion Compensation, which offloads rendering and AA work to the GPU, allowing you to use a slower, cheaper, cooler-running CPU than if you were just using XVideo or OpenGL to display the images. My recommendation is to go with a G33 motherboard and an inexpensive but pretty decent Pentium Dual Core E2x00 CPU if you intend to use the MPEG-2 codec for your files and can take advantage of XvMC. Also, if you prefer to not run any proprietary drivers, stick with an Intel platform for the present no matter what codec you choose as the open-source ATi driver is not currently able to do 3D and video reliably on newer hardware. If you are going to be using a non-MPEG-2 codec, get a Core 2 Duo E7200 or one of the E8000 series CPUs.
2. An all-AMD system can give you more hardware features for less money than an all-Intel setup and also can be more power-efficient. If you intend to use a video codec that is *not* MPEG-2, then I would go this route as you will be using XVideo anyway. I'd suggest an AMD 780G board instead of the 690G as the 780G is much more powerful and not that much more expensive. You will need a reasonably stout CPU like the X2 5800+ to decode and deinterlace CPU-intensive codecs such as H.264 using XVideo.
ATi's proprietary drivers are decent today but lack some features available in NVIDIA's and Intel's drivers, such as proper XRandR support and XvMC. They work very nicely with XVideo, though. There is 2D support for the 690G and 780G with the open-source Xorg ATi driver but 3D and video is spotty. It's coming, but not here yet.