I was able to pair the devices using bluetoothctl as you describe. It paired successfully. It connected and then disconnected. I attempted to repeat the process again by disconnecting on the phone and now nothing works. The phone says not connected and Edison still says connected. Below is the initial sequence.
[CHG] Device F8:0C:F3:F2:95:FF Connected: no
[bluetooth]# pair F8:0C:F3:F2:95:FF
Attempting to pair with F8:0C:F3:F2:95:FF
[CHG] Device F8:0C:F3:F2:95:FF Connected: yes
[bluetooth]# connect F8:0C:F3:F2:95:FF
Attempting to connect to F8:0C:F3:F2:95:FF
[CHG] Device F8:0C:F3:F2:95:FF Paired: yes
Pairing successful
[CHG] Device F8:0C:F3:F2:95:FF Modalias: bluetooth:v000Fp1200d1436
[CHG] Device F8:0C:F3:F2:95:FF UUIDs:
00001105-0000-1000-8000-00805f9b34fb
0000110a-0000-1000-8000-00805f9b34fb
0000110c-0000-1000-8000-00805f9b34fb
0000110e-0000-1000-8000-00805f9b34fb
00001112-0000-1000-8000-00805f9b34fb
00001115-0000-1000-8000-00805f9b34fb
00001116-0000-1000-8000-00805f9b34fb
0000111f-0000-1000-8000-00805f9b34fb
0000112f-0000-1000-8000-00805f9b34fb
00001132-0000-1000-8000-00805f9b34fb
00001200-0000-1000-8000-00805f9b34fb
00001800-0000-1000-8000-00805f9b34fb
00001801-0000-1000-8000-00805f9b34fb
453994d5-d58b-96f9-6616-b37f586ba2ec
936da01f-9abd-4d9d-80c7-02af85c822a8
Failed to connect: org.bluez.Error.Failed
[CHG] Device F8:0C:F3:F2:95:FF Connected: no
[bluetooth]# connect F8:0C:F3:F2:95:FF
Attempting to connect to F8:0C:F3:F2:95:FF
Failed to connect: org.bluez.Error.Failed
This is what I get now when I try and repeat the process
root@Papoose:~# rfkill list all
0: phy0: wlan
Soft blocked: no
Hard blocked: no
1: brcmfmac-wifi: wlan
Soft blocked: no
Hard blocked: no
2: bcm43xx Bluetooth: bluetooth
Soft blocked: no
Hard blocked: no
3: hci0: bluetooth
Soft blocked: no
Hard blocked: no
root@Papoose:~# hciconfig hci0 up
root@Papoose:~# bluetoothctl
[NEW] Controller 98:4F:EE:03:1F:2E BlueZ 5.18 [default]
[NEW] Device F8:0C:F3:F2:95:FF Nexus 4
[bluetooth]# show
Controller 98:4F:EE:03:1F:2E
Name: BlueZ 5.18
Alias: BlueZ 5.18
Class: 0x000110
Powered: yes
Discoverable: yes
Pairable: yes
UUID: PnP Information (00001200-0000-1000-8000-00805f9b34fb)
UUID: Generic Access Profile (00001800-0000-1000-8000-00805f9b34fb)
UUID: Generic Attribute Profile (00001801-0000-1000-8000-00805f9b34fb)
UUID: A/V Remote Control (0000110e-0000-1000-8000-00805f9b34fb)
UUID: A/V Remote Control Target (0000110c-0000-1000-8000-00805f9b34fb)
Modalias: usb:v1D6Bp0246d0512
Discovering: no
[bluetooth]# scan on
Discovery started
[CHG] Controller 98:4F:EE:03:1F:2E Discovering: yes
[bluetooth]# pair F8:0C:F3:F2:95:FF
Device F8:0C:F3:F2:95:FF not available
[bluetooth]#