These 2 articles were posted on tennis.com - I thought there were pretty interesting takes on the way that the rankings system works. They're about the WTA for the most part, but they touch on the ATP rankings, and the issues are basically the same.
For me, any decent tennis ranking system has to have three things:
1. Circularity: It should run over the course of a year instead of starting again at the beginning of the season, which skews the early results too much. Seems obvious, but remember that the ATP in 2000 actually wanted the Race to take the place of the regular rankings, another case of someone taking leave of their senses. (Measuring over two years, the way Nadal wants, or even just six months is also possible, but I think a year makes perfect sense for tennis given that it coincides with the season.)
2. A level playing field: Finding some way to compare players on an equivalent basis, so that Serena’s four tournaments aren’t judged beside Wozniacki's 24 without accounting for the difference. This can be an average or Best Of whatever, or something else. I’m split between the two, but they both basically do the job without being too complicated.
3. Quality control: In practice, this means bonus points. Winning a tournament beating Serena, Venus and Clijsters along the way is not the same as winning a tournament beating Pironkova, Radwanska and Kvitova along the way, and the rankings should reflect this.
I'm not sure that I agree that things need to be changed as the author states - the issue of Quality control in particular. I think that the idea of bonus points for winning against higher ranked players isn't necessary. Sometimes you get easy draws, and sometimes the draws are difficult, but that generally comes out in the wash.
The thing that I think is most wrong about the current system is that getting to the finals gives you 60% of the points that you'd get by winning the tournament (e.g. 1200 points for the finals of a Slam and 2000 for winning).