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no.. the "problem" is itunes does not back up individual changes in an app's data store, it simply backs up the whole application again. apps like goodreader or comic apps tend to modify their internal data (marking an issue read, or using a 3rd party app to upload content) that itunes isn't aware of. these apps also tend to deal in large amounts of data (people store 100 issues of a comic or dozens of large pdf files). so each time itunes goes to back up, it has to back up all of goodreader or comiczeal again. you mark another issue read, itunes backs it all up again. it really can't be avoided, itunes is doing what it was designed to, back up your changed content. if you want shorter back up times you store fewer issues of comics or a smaller library in goodreader. or you disable backups entirely and lose out on the protection.
if itunes knew how to manage each app's data (it doesn't) it might be possible to code it to only backed up changed content, but because each app can store its data however it wants, it's forced to back up the whole chunk again. fewer large files or many small ones, doesn't make a difference.
my advice, hook up your iOS device before you go to sleep and hit sync, it will be done when you wake up. i never have a problem waiting for backups.
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