Why did my sync with my new phone bring in such old data from my apps

I recently upgraded from a 3GS to a 5S. Before activating the 5S, I synced my 3GS in iTunes. When I activated the phone and did my first sync with it, the data in all of my apps that store data was very, very old. I use Calengoo, for instance. The calendar that was imported to my new phone looked as if I'd last updated it in September 2013, despite the fact that I back up and sync that calendar regularly. My online google calendar was up to date, so I could rectify that situation without much effort.
I also use a reminder program called Due. The reminders that were imported were similarly the ones I'd had in the phone last fall.
I use Balance Pro to keep track of my bank balances. The accounts and information in that app are also very old.
I still have the apps and current info stored on my old 3GS. Is there any way for me to import them to my new phone so that I don't have to manually re-enter all that data?
As a side note, some of the apps on my old phone were not transferred to my new phone at all. Google maps and IMDb are the two that I recall off the top of my head.
Thanks for any help,
Chris

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