The PDF version is nice as the main problem with the online one was the small page size.
How do you set up the documents originally? For the PDF version it would benefit you to use proper page layout software which would not only reduce the PDF file size but also stop the type from appearing bitmapped. You could then just rasterize the PDF file for the online version (I assume you need Jpegs for that).
Just out of interest, check out
http://www.gamerzines.com/ to maybe get some ideas to how they do things. Yes I know they are a fully professional outfit, but it might help you.
A note to Nat. If you save out the PDF, you can view the spreads properly in Acrobat by selecting View>Page Display>Two-up and make sure you have Show Cover Page During Two-Up checked.