I just thought I would share what I think is an interesting observation.
Since moving from the first generation iPad to the new 3rd generation, I found out that I now can sync without any problem one of my large database (around 11000 files, some quite large).
I had stop for a while now syncing that database, usually only do sync on my daily database (tickler files, meeting files, etc - no more then 500-600 files) because of the frequent crashes and database corruption (on the iPad only!).
I am not sure if this is related only to the new iPad having more RAM (iAnnotate also stop crashing when sending large annotated files back to DTTG), but clearly this makes for a much more useful workflow.