2 games in and it seems to me that the largest issue with Vicky 3 is that the systems are too generalized.
In US history, the abolition of slavery was the defining conflict of a century which involved unfathomable effort and resource expended on both sides. Vicky 2 modeled this by making it impossible to abolish slavery as the US and launching a unique civil war after a number of special events. Vicky 3 was supposed to model this by making the generic landholder interest group so upset at attempts to abolish slavery that it lunched a generic civil war. In my latest game, I abolished slavery within 5 years with nothing but light grumbling from the generic landholder group.
My other game was Japan. It felt just as generic as any other country; barely any flavor to capture the drama of the Meiji conflicts.
Other minor issues I have:
Far fewer provinces than Vicky 2, makes playing small countries less interesting.
Very much as a command-economy style that we see in other strategy games. Somewhat less so, but it's closer to generic strategy games than it is to Vicky 2 in that regards.
Plenty of other people have already mentioned how bad the UI is.