What your biased analysis fails to take into account is that Nadal skipped a slam and a Masters - the first one due to injury. That is a lot of points that he would have likely have accumulated that he didn't. Given his records at AO and Miami it is likely he'd have had at least 1500-2000 more points to his tally. That (and the Wimbledon loss) is one of the key reasons it is so tight - not because Novak was somehow way better than other no.2s have been in the past...
The fact is it is not numbers that matter as much as types of titles. 2 slams and 5 masters > 1 slam and 3 masters by a LONG distance. So yes, last year with everyone having one slam there was more of an argument over who had the best year/ "co-champions". This year, there isn't. Just like Federer winning everything in sight post USO in 2011 didn't make Novak's year any less amazing, the same is true for Rafa this year - 2 slams out of 3 played = best year.
It's very dangerous to evaluate players based on what would have likely happened if ...
But, since you like arguing in the woulda, coulda, shoulda realm, if Nadal had played in Australia, then he wouldn't have played the South American golden swing, which he hadn't played since 2005. By not playing Australia, he was not too spent to go and win 900 points playing on his favourite surface against weaker opponents than he would have faced in Australia. 900 points is more than a grand slam semifinal. It's not obvious that he would have made the final in Australia after 7 months off. We just don't know.
Also, if he played Australia and Miami, then he would have had more points going into Roland Garros and Canada. So very likely he would have seeded higher, so Novak would have played him in the finals of both, not in the semifinals. Novak would have earned 720 more points, bringing the difference to only 50 points!
So you see the danger of going into hypothetical scenarios? Two can play that game. And nobody knows what would have happened.
We have to go with what actually happened, which, as I explained in my post with numbers, is that Rafa beat Novak by a nose for the year-end #1. But Novak outperformed Rafa in ITF events by quite a large margin, not to mention that he actually commited to play all the ITF events, not only 60% of them, and actually did remarkably well in all of them, noto only in 40% of them.
One of the most important achievements of the ATP was the introduction of computer rankings and objective ranking points, to avoid subjective judgements of what's more valuable. Of course 2 grand slams are better than 1 grand slam and the WTF. And the rankings show that. But the ITF gives weight, for their award, to overall performance and commitment to ITF events. They made the right decision,and I admire them for withstanding the pressure to do otherwise.