nibali's progression is undeniable and very easy to notice.
his biggest weakness was several days in a row making big efforts for GC. in the 09 tour, which was the first GT he rode for himself, he struggled on stage 17 and 18 (the grand colombiere and the annecy time trial) as they came after the verbier MTF where he was third and another mountain stage on stage 16.
his performance on ventoux on stage 20 was already good again and imo he only lost time because he burned to much energy attacking the second tier contenders group and bridging a fairly big gap to contador and schleck following them for a while until they slowed down and were caught by the group nibali was in.
http://www.youtube.com/watch?v=M11zpoaxt3w
attacks around minute 10 and catches contador and schleck around minute 12.
On the giro 2012 he once again struggled with consecutive days on the mountains. was great on the stage to Asolo which he won with a 40k long solo effort on the descent and flat after being the one breaking the race apart on the monte grappa. the following day he struggled on monte zoncolan.
same happened with him being great on the stage to aprica and struggling on the following day on the Gavia- Tonale stage. however it was obvious after that giro that his climbing was better then it was the year before.
during the vuelta he only truly cracked on the stage to the alto de cotobello which came after the pena cabarga and lagos the covadonga stages where he was good. he was then very good on the bola del mundo stage.
his performance on last years giro is imo a bit underrated due to the margin he lost to contador and because he lost his second place to scarponi. but truth be told he only had 1 bad day on the entire race which was the finestre stage, on the val de fassa stage he lost time but mostly because of his aggressive tactics against contador which made him waste way to much energy. it must be said tho that he did a very good time trial the day after cracking on finestre.
imo this are clear signs of improvement over the last 3 years.