When viewing books on the iPad there are a number of options, the two biggest being PDF with Goodreader and Kindle formatted book with the Kindle software. Today we’re going to take a look at the pros and cons of both options.

###Scenario
My use case is that I want to have the books I read backed up online but more than that I want to be able to read them and make notes that sync with the books. I want these notes to be available on my iPad and iPhone and on my Mac (and any other platform for the future).

###Goodreader
If you haven’t heard about Goodreader before then you must have been living under a rock. Goodreader is the best document viewing application on iPhone or iPad. It let’s you view and annotate PDF files along with many other features which I’ll cover in a future review. PDF files are a safe bet because they’re just everywhere. You can read them on any platform and the notes are viewable everywhere.

The biggest feature that makes Goodreader a point of discussion today is its sync feature with Dropbox. The sync is even two way, so you can make a note on a PDF file and save it back to Dropbox when you’re done. This two way sync is what makes Goodreader and PDF files suit my needs. Annotations show up on my Mac once the files have been synced back to Dropbox.

The sync isn’t quite perfect though. You’re not opening the native Dropbox version of the file (it’s just a limitation of iOS) so getting your notes synced means syncing the whole file back to Dropbox, not just the new notes. In the case of one file I worked with recently that meant 97.5mb of uploading needed to be done. This means syncs aren’t fast from iOS so you’re not going to make a quick notation and save it, you’ll need to make sure that you’ll have the time to upload the changed file.

Once the new file is uploaded it syncs back down to your main computer really quick. I’m not 100% sure but Dropbox must know that it’s just an incremental change and only sync the changed bits. Viewing the notes on OSX is a simple process of opening them in Preview and then clicking on the ‘notes’ button in the lower right hand corner. Preview also lets you make notes easily but again to see them on your iOS device you have to open Goodreader and sync the folder which requires a scan and download. This is faster since typical download speeds far exceed upload speeds but it’s still a manual process that you need to remember to perform.

The manual process also means you’ve got a possibility of sync conflicts. You could make a note on your Mac and not sync right away. A few days later make some notes on your iPad and then sync and you’ve got a conflict. Goodreader is set to ask you what you want to do with the conflict but it comes down to a manual process. You’ve got to keep one file and throw out the other, create duplicates or leave it unresolved. I’d really like to see it sync every time you open the program though if you’re syncing large amounts of documents (2GB of books for me) it could take a bit of time.

###Amazon and Kindle
The second option is purchasing your books via Amazon’s Kindle service. Amazon provides their Kindle software for every platform I’m on, OSX iPad and iPhone. The software ubiquity means I’m not giving up access to my books because it’s on Kindle. At this point it’s also pretty safe to assume that Amazon is big enough that the Kindle software won’t be going anywhere any time soon.

Kindle books come with Whispersync which is really just a two way sync. In practice this means you can read a bit on your iPhone and when you open it on your iPad it will sync forward to the page you were on.

This sync feature also extends to the notes you make in the book. Make a note on any version and it will be synced to all versions. All of the syncs are incremental too so you’re not waiting for the software to save 97mb stuff each time you want to sync notes.

The big draw back to Kindle is that the sync always moves you to the furthest ahead page. So in a technical manual you could be reading one section for reference and jump back to another portion of the book but it will keep trying to sync you to the furthest page. This certainly makes sense for reading fiction books since you consume their content in a linear fashion, but that isn’t always the case for technical content.

The second item I don’t love about books on the Kindle is that the table of contents sucks. On OSX you can have a bookmarked copy of the contents sitting on the site of the reading area. In Goodreader a simple press at the bottom of the screen and you can navigate the contents through bookmarks easily. The Kindle formats I’ve dealt with require you to press and navigate to the contents pages then flip through till you find the page
section you want then jump to it. Sure it works but it’s not nearly as smooth at the PDF files provide.

###Option Three
There is a 3rd option, storing notes in text files. It would be a simple matter of recording which page and copy/paste any required text to the text file. WriteRoom makes searching files easy on iOS and nvALT does the same for OSX. Text files are also readable on any device, they’re light weight so syncs are quick.

The issue with this is that the notes aren’t directly linked to the text in question. You can’t just go in to the file and click on it to bring up the exact location in the book that the note pertains to. You’ll have to open the text file and then the book then go to the page in question. It just seems like a lot of steps to me, which means I’m less likely to do it.

###Which One?
Each option has it’s draw backs. Using the PDF method you’ve got to upload the whole file each time you make a note and want it synced. Using the Kindle method you’re dealing with pretty terrible table of contents navigation but super quick syncing. Using text files means multiple applications running and no direct link to between your notes and the corresponding text in the files. Really what I want is a solution that syncs as fast as Kindle books but has bookmarks like PDF files. Anyone have other suggestions?