Personally, I see two logical options for how to handle the skill tree:
1. Don't touch the skill tree at all, because it's a tangled mess, but considering the reworked Factions, completely ignoring it isn't an option, which leads to the second option...
2. Overhaul the skill tree and finally make it sensible – balance the number of perks, remove confusing connections between skills, and make the progression of common skills uniform for everyone. Considering that there are 4 elemental magic schools, we can create something significantly different from other projects. Furthermore, hero progression is a part of role-playing the character – it's an important and far from insignificant aspect. Adapting this part of the game to the new Factions will only be beneficial – it provides room for creativity, again emphasizes the project's individuality, and allows for a more immersive experience in the new setting.