Flash TTL has its benefits as well as its drawbacks. I prefer controlling my flashes, hence I use the YN560 III's with the 603N II triggers for off camera flash. My YN565EX I use mostly hooked to my camera.
Very soon, I'm going to get the YN560 TX controller (trigger) for my YN560 III flash, plus another YN560 III.
Yongnuo only makes two types of flashes with built-in radio triggers: manual-only flashes (YN-560III & YN-560IV). The YN-565EX/568EX/500EX (and MkIIs) models
do not have a radio receiver built in.
The built-in slave modes on the YN-565EX are optical (light-based), not radio. It can be used in Nikon's CLS (or Canon's wireless eTTL) system, and can be used as a "dumb" optical slave to fire from a flash burst from any flash (similar to SU-4 mode on a Nikon speedlight). Optical-based triggering, though, has range of line-of-sight requirements that become more stringent and restrictive if you're shooting outdoors and in bright sunlight.
The receiver on the YN565EX is
optical. It responds to pulsed light signals sent from the master flash mounted on the camera. This makes it compatible with Nikon's CLS, which is optical.
The transmitter on the YN560TX uses
radio signals, not
optical pulses, to communicate with the flash. You need to attach a
radio receiver to the YN565EX so that it can receive the
radio signals from the YN560TX.
Long and drawn out, I know...but I hope it answers your question about which one to get.
Let us know what you decide.