I said to my friend when the draft was done that NaVi would lose due to having no stuns
If the enemy team pick 5 heroes with 20 stuns and you pick that weaksauce lineup you deserve to lose
It is true that it is very, very hard to win a game of dota without disable. But even with disable, C9 was still going to get 3 or 4 BKB's up by 30 minutes. Na'Vi had the gold lead on the heroes that mattered.
In the end, C9 made better decisions. They prioritized Rosh, made sure to check it regularly and had it warded. Na'Vi never had rosh warded and never contested a single Roshan. How many fights were lost explicitly because of the aegis + cheese advantage that could have otherwise turned into objective pushes for Na'Vi? At least 2. C9 also didn't have a knucklehead Xboct on their roster who sometimes seems to be oblivious to the fact that there are enemy heroes on the other team that would like to kill him.
Lack of recognition that Rosh was the difference was a problem. Lack of warding at and around the rosh pit was a problem. Disable was a problem (but less so). Poor decision-making was a problem. They also really didn't get much of anything out of that Wisp pick.
Even with all the problems, they probably still win if they don't give up every rosh for free. But if the queen had balls, she'd be king.