Voila,it was 2006,Nadal's major ticks were butt picking and sock adjusting,he didn't add many ball bounces,he didn't towel off after every point,he didn't adjust his hair after every point and he certainly wasn't as adamant as bottles as he was latter on. It's not tough to see that he has added more and more things to his routine,hence he wastes more time now than he did in the past. If we want a fair analysis we should see how much time Nadal took and takes on regular balls(not bp's or other key moments in a match,like in a tiebreak and such cause everybody slows down in those moments) in the 04'-09' period but that would be really,really boring but I can tell you right now,he has more rituals and takes up more time in 08'-09' than he does in the 04'-07' period.
As I said before,as he got better and more pressure was put on him he made up more and more rituals,as the OCD sufferer that he is,to keep his calm in the big moments. Nadal thinks he needs to do a-b-c to keep his focus (and when a is butt picking and c or d is watter bottle arrangement,both embarrassing,you can see why I say he is OCD) which isn't bad on its own but when it is a to f,g,h then it really gets drown out and he goes over the time limit.
I don't think Nadal said to himself "I know,I'll incorporate more and more routines to slow down the game,some of which are embarassing,just to throw off my opponent,annoy fans,umpires and everybody in the game". Unless someone penalises him REPEATEDLY(and by repeatedly I mean a few times per match for several matches-if the takes too much time). OCD'er don't let their habits go just like that,they need some help and outside intervention.
The ONLY gesture which Nadal did let go was the sock thing but the rest he just kept piling on.
Watch his match with Fed in 04' for example. He was a energic young guy who couldn't wait to serve and get out there but he calmed himself down with these things(tony said he didn't teach him any of these things he just told him to try and steady himself),these rituals until it blew out into a minor case of OCD(not that uncommon among athletes). It's one thing to have superstitions,habits but Nadal takes it to the next level by making sure that he does things his way on court,as I said before a-b-c and so on,even things that have nothing to do with tennis and which are embarrassing(butt picking and the bottles).
This is Nadal(after he rearranges the bottles of course):
http://www.youtube.com/watch?v=3mEGDNHcHoU