I think by Vettel being champion it boosts hims a bit because people have the perception that 'the champion always deserves it', they do, but it doesn't mean they were the best driver in given season.
I'm not sure about Raikkonen being in 3rd either, I think he's benefitted from the (slightly) gifted win in Abu Dhabi and the fact that even though his team-mate regularly outqualified him he usually beat him in the race because Grosjean couldn't get around the first lap half the time.
Don't get me wrong, I think both drivers should be in the top 4, I just think they've been somewhat flattered by the factors mentioned above.