The first two charts are the most used skills. You can see what the 6 skills are in the table at the bottom. It's only to illustrate the differences between the classes.
Factors contributed to changes and status quos, one example in parantheses.
Skills buffs (DH Perfectionist)
Skills nerfs (Wiz Storm Chaser rune)
Inaction from Blizzard (Monk)
Better gear available due to deflation of mid-high items and increased drop rate. (Witch Doctor increase skill distribution)
Monster Power system (Barb Thrive on Chaos)
Yeah, it's 1.0.4. DH's Vault (Trail of Cinders) is high, which it wouldn't have been in 1.0.3 and prior. While this does show a lot of build focus, I would very much like to see a similar chart for 1.0.3 to check if the scores have gone down or up... and another one a couple of weeks after 1.0.5 hits to see how the changes there will change things. Where did you get your data, anyway?
I do find it funny how few of the "cookie-cutter" skills I end up using, and how good some of the sub-1% ones are (Fierce Loyalty is clutch in some builds, for example). Some of them are obvious, though, such as Ballistics and Pacifism. They're either too situational to be good or reliant on skills that just don't have the beef to back it up
Ideally, you would want every skill (and potentially every rune) to have an equal amount of use. This shows this is clearly not the case, and there are skills which are deemed a necessity (War Cry for Barbarians)
Well yes monks have it bad, or good depending on how you look at it. The specific runes are so powerful there's nothing that really comes close. It's not like we want to do the cookie cutter but we don't want to be woefully inefficent either.