^First: MegaZine3 cannot handle PDFs directly. They needed to be converted into swf before. So swf is most probably the best way.
You should try different parameters. that are available on bookd, page and element level.
Like "buffer":
http://www.megazine3.de/doc/Page#bufferIf you use batchpages, this will be the first flag of the settings parameter; like
settings(true, false, false, false, false)">
If you build the pages one by one (not with the batchpages plugin), then you should try:
<page buffer="true" >
You also should test with buff_aa and buffer_animate set to "false".
Check those parameters availble and see if there are other options that could improve the performance of your books.
Another way is to reduce dpi during convertion...
At the end it all depends on the number of vectors (characters) on the page. So if you could use bigger fonts and more pages would also help ;-)
And as another approach: you could use small, low quality jpg images for lower zoom levels and only swithc to higher quality jpg or swf files if the zoom level is set higher than the trigger level defined by scale.