I liked the way this idea worked in the Caesar/Pharaoh games.
I am not exactly sure how you are planning to implement things, but if you are having it so the skills/abilities are built up over time and carry over from mission to mission, than I would suggest the following.
If you have your skill tree split into two main branches (military and science) you could have the game auto adjust based on the amount of skills in each category, and have the cost of each skill increase significantly each time. One of the benefits of this is it makes the player choose one path over the other, while not completely limiting their ability to go into the other side. The player could evenly invest in both branches of the tree, but would never be able to reach the top most of either side (jack of all trades, master of none). They could invest heavy on the military side, so the cost for the most basic science skill would be less useful than the next level in military, and the same would go for investing heavy on the science side.
Now going back to the Caesar/Pharaoh mission concept. The game could auto choose the next mission branch based on the difference in the skill tree. If the player has 10 points in science and 2 in military, it could go towards to the more peaceful/diplomatic mission instead of the military based mission. If the player has chosen a more neutral skill path then there could be a separate mission for that as well.