iTunes: no more support for Aperture / iPhone sync??

Which version of iOS do you have installed on your iPhone?

For my iPad I can still sync from my Aperture library to the iPad, but I did not update the iPad to the problematic iOS 9.3 version.

I cannot test this with the same iOS version you are using, because I am using a hotel Wi-Fi right now and don't want to risk an update while traveling.

Have you waited long enough? Sometimes it takes a long time for all photo libraries to appear in iTunes. Try to quit both Aperture and iTunes and see if the problem persists, after you restart the Mac. Is your Aperture library on a drive with a supported file system (MAcOS Extended (Journaled) )

It may help to remove the iPod Photo Cache from your Aperture Library. iTunes: Understanding the iPod Photo Cache folder

As a work around, export the albums you want to sync as a new Aperture Library and then open that library in Photos for Mac, so you can sync them from Photos to your iPhone.

I too am having the same problem. I'm on 9.3.1. Before this, when synching my iPhone, I could select synching with Photos or Aperture albums. Now when selecting photos to synch, I'm only told that iPhone can synch with Photos in iCloud. I hope someone knows a workaround.

I figured it out!

Just turn off the iCloud synching preference in Photos and the synching then reverts back to letting you select between Aperture and Photos synching ON YOUR MAC.