The Qatar Airways business class cabin on the A330 is far more comfortable than Emirates, offering greater leg room and seat width. The seats are enclosed in hard shells and are angle lie flat. Qatar six abreast versus Emirates seven abreast in J class.
I find the Qatar service to be far more excellent than Emirates and their A330s are all newer than the EK equivalent. Skytrax has some decent reviews about the onboard services of both.
As youve all ready pointed out, QR does not offer a door to door limo service. Furthermore, the connecting flight from Doha to Nairobi is usually on an Airbus A320 or A319 occasionally. The latter has the same business class seats as the longhaul A330. However, the A320, which is used most frequently on the route, employs the old style recliner armchairs in business class, which are actually very similar in recline to the seats used by Emirates on their A330! The Qatar seats are generously wider though.
Given the choice, I would elect Qatar. Very worthwhile to try out their service.
Good luck.