I am not a big fan of the random skills upon leader level up. When I am in dire need of a specific skill, I find myself saving and reloading over and over just to get that skill to appear (usually done to get an expert explorer to explore ruins with more RNG involved, haha). I would much rather already know in advance what my leader will be capable of in the future instead of rolling the dice. Being a skill tree, it could be made so players are forced to choose one skill over another, similar to the culture perks. This would also allow for ship related skills to be organized together into a tree and colony management skills to be organized into their own as well. Let me know what you think.
Yeah I see your point, it gets messy at times and doesn't make much sense as it becomes harder to specialize your leaders. I resist that temptation but I will concede that many players will do exactly that. Therefore it might make more sense to simply give them more input in how the leader advances as they can do it by this method instead.