Not to be critical of other people's personal choices but I wouldn't dream of syncing any more than the 10 or so books on my to-read list. Everything else sits in the iTunes library but I stop syncing them after read.
I find the slow sync of the iPad to be the biggest annoyance. The backup length is directly related to the number of files in the iPad. Currently it seems to back-up everything instead of using incremental back-up of changes. Maybe once they fix that I'll reconsider, but for now I tend to manage files carefully to avoid 15 minute back-ups.
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