Absolutely, there is so much more than just a simple number to be considered. And unless you have a formula for calculating the strength of a squad and what the return on that should be (taking into account of course the fluctuating squad strengths of all the other teams in the league as well as things like injuries, suspensions and transfers) then you will never have a definitive answer as to whether a team or manager has over- or under-performed, or done better in one situation that in another.
In short, it's an opinion, and while at the moment its easy to come to the opinion that Everton 'should' be doing 'better', it's not easy to define how much better. Logic suggests that Martinez should be doing better at Everton than he did at Wigan. Is he? League positions suggest so. If so how much better should he be doing with Everton to be 'enough'? Because just doing 'better' clearly isn't enough. He couldn't organise a defense at Wigan so I'm not sure why the hell people expect him to be able to at Everton. He's got his team playing good attacking football and he is popular with his players while still struggling for consistency and can't instill a defensive mindset into players. This is the same as at Wigan, so it sounds like he's performing exactly as should have been expected. Is he under-performing as a manager, or is too much expected of an average manager? Can a team with an average manager ever be more than average?
There's a lot of playing devil's advocate there of course, but there's a lot more to consider when weighing up performance against expectations that just a simple statistic.