Flexibility. As El Jojo above said, V2 has more focus on internal country development. However, EU3's map has many more countries (including lots of small provinces), prospects for colonisation, etc. You can get a small one province minor nation in EU3 and transform it in a big blob to rival France, while in V2 this is not likely without resorting to gamey tactics and infamy wars.
However the longer time frame of EU3 is, in my opinion, not necessarily a huge advantage. At least in my experience, I often spend a lot of time in V2 checking my POPs and industries, so I run in a lower speed and constantly pause. In EU3 depending on the country you play, there are long periods of time - sometimes years - when nothing much happens and a century goes by really fast while you wait for your infamy to decrease or your stability to rise.
In any case, they're two different games - both good. If you care about content, EU3 with all expansions is definitely more polished and offers many more things to do than V2 at this point.