Motion relies VERY heavily on the graphics card, so of course the 5200FX is slowing you down. Are you on a dual G5 or single? The dual should be quite a bit faster, knowing Apple apps. The 9800 should speed things up because it has a faster GPU plus more RAM. If you can (money) get a 9800 Special Edition because it has 256MB RAM, which may be used by Motion if you're doing big projects.
Edit: Or save $50 on the above offer 😀