No syncing of documents makes management difficult at best, because you could have multiple versions on computer, iPad, iPhone, and cloud. (I think what is even worse is that a lot of iPad bloggers, tech reviewers, and app publishers are using the word "sync" a little too loosely. Apple refers to the process as "File Sharing", but a lot of other people are using the word "sync" which is very inaccurate.)
Editing in place on a cloud doesn't work as an option either. Because not all applications (the iWork suite for example) support opening remote servers. Also you would have to rely on the speed and reliability of the network connection, or even having a network connection.
If full document sync is out, and in particular syncing an entire directory, then you start to consider other options:
Having all Documents vs just Reference Materials and Current Projects:
Maybe instead of trying to have all of your working documents on the iPad, maybe you should consider having an important subset of files. And if editing the documents is cumbersome because documents become "out of sync", perhaps the iPad should be used primarily as a consumption device, for reference and occasional editing.
For example, instead of having the entire "Network Documentation" folder on my iPad, maybe I should just grab the most important documents. Similarly, does it make sense to have the OmniGraffle version of floor plans or just a PDF for reference purposes?
This workflow would also imply that you just need a volume of reference materials, a PDF reader, and a workflow that prompted you to update the reference material.
And of course, this leads to the next problem. Now you have to maintain two (actually more) sets of data, the original working files, and a directory of "important reference" materials to be sent to the iPad. Then you have to take some of the documents and save them as PDFs for the reference folder. And finally, you have to remember to add new reference materials to the iPad folder, and update a PDF reference document when the original content changes, and then upload the changes to the iPad.
This is crying for a MobileMe syncing solution. Something that allowed for local storage of documents to be synced in the cloud. Apple does it with calendars, contacts, hopefully they will add documents. It would certainly help sales of MobileMe (which the Apple sales clerk asked me no less than four times if I wanted to buy as I purchased my iPad).
The problem is a little better if your computer and iPad are on the same wifi network, as several apps allow you to mount over wifi.
AirSharing HD and GoodReader both allow you to open a document in it's storage area in an iWorks app, and that helps, but once the document is edited in an iWork app, you are stuck in that loop of multiple versions of an app and the kludgy way of moving the docs out.
Other Considerations:
Backup
Speed
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