You should be able to open your iWeb '08 site in '09 with no problems.
I am experiencing screw ups with links in custom navigation menus. When I make changes, iWeb decides to alter these and they appear in the published version completely different than they are in iWeb.
This happens in a, seemingly, random fashion.
To correct this I have to delete the item, save, quit, restart, relaunch, add it back, save and publish.
This is all rather time consuming and has not removed my doubts about the competency of the developers even without considering the problems with the FTP and MobileMe publishing.
I am also experiencing random screw ups in HTML snippets on pages that previously worked OK and iWeb has messed up without me going near it. I had to fix one of these this morning before I could direct someone to a page where this had happened.
I really can't understand why Apple continues to release software that doesn't work as planned.
Even more incomprehensible is the time it takes to come up with a fix that doesn't fix much at all and the total lack of communication with the users.
When I make one of my many mistakes, I admit to it and try my best to address the matter. This action is defined as taking responsibility and appears to be lacking in our society in general as well as certain software developers in particular.