I downloaded the new version of pages about a month ago. Today I tried to open documents that I created and saved with the new version and received a message that I needed to download the new version. The app store shows the download. HUH?!?

Are you launching Pages from an icon in your Dock? Installing the update does not change the Dock icons & it does not remove the older versions. Go to your Applications folder & launch the new Pages from there then right-click on the Dock icon & select Options > Keep in Dock.

Installing new versions of iWork has never replaced existing versions. This is nothing new. The only thing new is that the '09 apps are moved to an iWork '09 folder if they were purchased from the Mac App Store. If they were installed from disk they should already be in a separate folder in Applications.

I'm not sure what you mean by it making accessing files more complicated. I have both Pages 4.3 & Pages 5.1 icons in my Dock as well as Numbers 2.3 & Numbers 3.1. I continue to use the iWork '09 versions for my everyday needs. As long as the new versions are in your Applications folder & the '09 versions in the iWork '09 folder, Software Update will not have a problem updating them even if Apple should come out with a new update for the '09 versions.

Because I have moved the new versions to an external drive & renamed the apps because I want '09 to be the default apps, I do have to remember to move them back to my applications folder & restore the original names before updating. But since you like the new versions this "complication" doesn't apply to you.