For wireless features, the biggest change comes from having to handle two 5 GHz radios. The setup wizard lets you keep the default Tri-band Smart Connect mode, or switch to Standard setup to manage the three radios separately.
Setup Wizard wireless choice
The Wireless > General screen looks like this with Smart Connect enabled. The only things you can change are SSID, Hide SSID and security related settings (from Authentication Method on down). You probably want to change the single SSID from its default if you didn't already do it during the Setup Wizard.
Wireless Settings - Smart Connect enabled
I was surprised to find WDS bridging enabled, even with Smart Connect enabled. The RT-AC3200 is the only of the three AC3200 routers to support WDS.
Wireless Settings - WDS
Wireless features continue to be one of ASUS' advantages vs. its competitors, at least for those who insist on being able to tweak everything. I was also surprised to see Wireless > Professional settings enabled for each radio with Smart Connect enabled.
Wireless Settings - Professional
If you disable Smart Connect, the standard controls appear for each radio. Like other AC3200 designs, each 5 GHz radio is limited to a subset of channels. 5GHz-1 supports only channels 36, 40, 44 and 48 and 5GHz-2 supports only channels 149, 153, 157 and 161. This is due to the filtering and other design tweaks required to keep the two radios from overloading each other. ASUS also includes channel 165, although it isn't of much use in 802.11ac's 80 MHz wide channel world.
Wireless Guest networks are supported for all three radios, with three profiles per radio with the settings shown below. Once again per-radio guest networks appear to be enabled, even with Smart Connect engaged.