I approve the graph system! When Anima first showed it to me I was dubious, then I realized the possibilities...
For those who didn't understand much, think like the unit / research advancement charts present in games like Civilization, see example image below:
I am not sure if the engine will allow it, but a very good feature was that you could set a "goal" and the game would automatically pick all the required previous nodes to reach it. This way for the more lazy players if you know that you want to be able to unlock the "Big Guns" perk at level 30 which allows you to use two bazooka at once, you set it and the game will take care of making the right choices.
All of this optional of course, you can still choose to manually make the choices. But I remember some people (rightfully) complaining for Loren when replaying the game for the 10th time, when they had a big levelup screen with 10 characters to level up