We're still using Indigo for the majority of our projects. The major reason is simply because the clients we're developing them for don't see any benefit to upgrading to 16.04 / Kinetic and don't want to pay for the time it would take to migrate and test everything.
As far as technical reasons go, the biggest obstacle is migrating from OpenCV 2 to OpenCV 3. There are enough API changes between versions that migrating is a significant task, especially if we want to maintain 14.04 / Indigo compatibility. Qt 4 / Qt 5 compatibility is a lesser issue but has also cropped up in a few places.
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