A simple auto-accepting BlueZ 5 pairing agent. WARNING: This auto accepts everything, be careful with it as it removes a lot of security in BlueZ!

auto-agent.py

#!/usr/bin/python

from __future__ import absolute_import, print_function, unicode_literals

from optparse import OptionParser
import sys
import dbus
import dbus.service
import dbus.mainloop.glib
try:
  from gi.repository import GObject
except ImportError:
  import gobject as GObject
import bluezutils

BUS_NAME = 'org.bluez'
AGENT_INTERFACE = 'org.bluez.Agent1'
AGENT_PATH = "/test/autoagent"

bus = None
device_obj = None
dev_path = None

def ask(prompt):
	try:
		return raw_input(prompt)
	except:
		return input(prompt)

def set_trusted(path):
	props = dbus.Interface(bus.get_object("org.bluez", path),
					"org.freedesktop.DBus.Properties")
	props.Set("org.bluez.Device1", "Trusted", True)

def dev_connect(path):
	dev = dbus.Interface(bus.get_object("org.bluez", path),
							"org.bluez.Device1")
	dev.Connect()

class Rejected(dbus.DBusException):
	_dbus_error_name = "org.bluez.Error.Rejected"

class Agent(dbus.service.Object):
	exit_on_release = True

	def set_exit_on_release(self, exit_on_release):
		self.exit_on_release = exit_on_release

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="", out_signature="")
	def Release(self):
		print("Release")
		if self.exit_on_release:
			mainloop.quit()

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="os", out_signature="")
	def AuthorizeService(self, device, uuid):
		print("AuthorizingService (%s, %s)" % (device, uuid))
		return

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="o", out_signature="s")
	def RequestPinCode(self, device):
		print("RequestPinCode (%s)" % (device))
		set_trusted(device)
		return ask("Enter PIN Code: ")

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="o", out_signature="u")
	def RequestPasskey(self, device):
		print("RequestPasskey (%s)" % (device))
		set_trusted(device)
		return dbus.UInt32(0000) #hard code PIN to 0000

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="ouq", out_signature="")
	def DisplayPasskey(self, device, passkey, entered):
		print("DisplayPasskey (%s, %06u entered %u)" %
						(device, passkey, entered))

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="os", out_signature="")
	def DisplayPinCode(self, device, pincode):
		print("DisplayPinCode (%s, %s)" % (device, pincode))

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="ou", out_signature="")
	def RequestConfirmation(self, device, passkey):
		print("RequestConfirmation (%s, %06d)" % (device, passkey))
		confirm = ask("Confirm passkey (yes/no): ")
    return

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="o", out_signature="")
	def RequestAuthorization(self, device):
		print("RequestAuthorization (%s)" % (device))
		return

	@dbus.service.method(AGENT_INTERFACE,
					in_signature="", out_signature="")
	def Cancel(self):
		print("Cancel")

def pair_reply():
	print("Device paired")
	set_trusted(dev_path)
	dev_connect(dev_path)

def pair_error(error):
	err_name = error.get_dbus_name()
	if err_name == "org.freedesktop.DBus.Error.NoReply" and device_obj:
		print("Timed out. Cancelling pairing")
		device_obj.CancelPairing()
	else:
		print("Creating device failed: %s" % (error))

if __name__ == '__main__':
	dbus.mainloop.glib.DBusGMainLoop(set_as_default=True)

	bus = dbus.SystemBus()

	capability = "NoInputNoOutput"

	parser = OptionParser()
	parser.add_option("-i", "--adapter", action="store",
					type="string",
					dest="adapter_pattern",
					default=None)
	parser.add_option("-c", "--capability", action="store",
					type="string", dest="capability")
	parser.add_option("-t", "--timeout", action="store",
					type="int", dest="timeout",
					default=60000)
	(options, args) = parser.parse_args()
	if options.capability:
		capability  = options.capability

	path = "/test/autoagent"
	agent = Agent(bus, path)

	mainloop = GObject.MainLoop()

	obj = bus.get_object(BUS_NAME, "/org/bluez");
	manager = dbus.Interface(obj, "org.bluez.AgentManager1")
	manager.RegisterAgent(path, capability)

	print("Agent registered")

	# Fix-up old style invocation (BlueZ 4)
	if len(args) > 0 and args[0].startswith("hci"):
		options.adapter_pattern = args[0]
		del args[:1]

	if len(args) > 0:
		device = bluezutils.find_device(args[0],
						options.adapter_pattern)
		dev_path = device.object_path
		agent.set_exit_on_release(False)
		device.Pair(reply_handler=pair_reply, error_handler=pair_error,
								timeout=60000)
		device_obj = device
	else:
		manager.RequestDefaultAgent(path)

	mainloop.run()

	#adapter.UnregisterAgent(path)
	#print("Agent unregistered")

Thank you for this! Closest thing to what I'm searching for so far.

Line 92's return indentation is incorrect.
Fixing this allows execution of the script, but import bluezutils fails on my fresh RetroPie 4.4 image with Raspbian Stretch even though bluez 5.42 is installed. Where do I get this module? pip install bluezutils doesn't help...

this appear to be the bluezutils you were looking for
https://git.kernel.org/pub/scm/bluetooth/bluez.git/tree/test/bluezutils.py

it is not working, i can send the pin but it is not checking if the pin are the same from both sides and pairing the 2 devices