I think they're both good airlines.
On Emirates' B777 aircraft, seating is 10 abreast as opposed to 9 on most carriers. However, seats down the back have rows of 2 on the window side, as the fuselage tapers in. I like these seats.
Service on both carriers is generally good. These two airlines have crew from all over the world, and the level of service depends on individual crew, just like every other carrier. However, I think it's better than your national carrier, Qantas.
Food is subjective. I always pre-order Indian vegetarian and I have enjoyed all meals on both carriers. Check airlinemeals.net if you are truly curious about what you'll be offered.
One thing I don't like about Qatar is that they often use narrow body A320 aircraft for flights from Doha to Europe. Check if Manchester is one of these routes. These aircraft still do have personal entertainment, but I personally prefer wide body aircraft. Not sure if that's an issue for you.
There are always people who hate either Dubai or Doha airport. I'm not a fan of the latter, but the new one is opening soon.
Really, they are both top-notch airlines as far as economy class goes. I read somewhere that Qatar is joining Oneworld alliance, so that might sway it for you if you want to collect the FF points. If that's not important to you, I would go by price and/or schedule. People will always complain about things but both EK and QR are solid carriers. I'm a loyal Skywards/EK traveller but fly QR if the fare is considerably lower.