1. Opportunity cost. Devs have limited resources, they could instead work on mechanics and dynamic content. There are so many more ways to play a country than there are ways to play a mission tree. So why spend resources on making content that will be played through three times out of a hundred instead of spending resources on dynamic content that could influence fifty playthroughs out of a hundred?
Mission trees also tend to be nation-specific, so development resources are spent on specific playthroughs of specific nations, rather than dynamic content that may apply to various playthroughs of many nations. So it's not an efficient, scalable use of development resources.
With nation-specific mission trees, countries are "missing" content until they get a DLC with content specifically for the country.
2. I would want England to play differently from Hungary organically from having different demographic, political, cultural, international, historical setup, not because they each have a scripted mission tree. However, if, through gameplay, England ends up in a situation similar to Hungary's at the start, then I would want England to experience the similar consequences and have the similar goals and tools and options as Hungary did. But that would not be possible with nation-specific mission trees. I don't want interesting content locked behind single, or a few countries.
3. Game mechanics and balance get designed around the mission trees, so it's not something tacked on that can be ignored. The mission tree paths are naturally tested more than other playthroughs of the same country, so the game tends to get balanced around the mission trees.
4. It's top-down design tendency that's in conflict with bottom-up emergent gameplay. Hypothetically, the mission tree designer might say, "It would be fun for the players to conquer x as y." and so that mission is added, but then the players complain that it's too difficult to conquer x, so the game balance gets tweaked to make that easier. So roleplaying believability, gameplay, balance all can get compromised like that to serve the mission tree narrative. It's backwards compared to the game saying, "Here's your starting situation and here are your tools, see what you can accomplish," which is much more interesting and fun, and to me, the main reason to play Paradox grand strategy games.
As I've described in #1, rigid scripted content exists in the place of dynamic mechanical content. The more of it means the less of the latter. I want less of it and more of the latter. I want gameplay enriched and countries differentiated by things like Societal Values, Control, religion, demographic makeup, resources, development, diplomacy, not scripted mission trees.