Going forward, it is likely I will remove the 5th faction skill tree (which will also remove the restrictions on some actions such as 'Strategic Command') . I mostly agree with Megas, and feel that the skill point sacrifices aren't really worth it. The whole thing never really worked as well as I hoped
I 'like' some of them, in the gameplay sense of having to invest into them to get all functionality and also gating some of it with player level, the problem with them is not only having less skill points for your favourites, but also less aptitude, which is killer.
Have you taken a look at the skill tree in SS+? Its really rather well done ... there's a lot of nifty stuff in SS+ and the skill tree is one of the best parts. To get round the fact that the level skills are balanced around less skills, on non-aptitude levels you get 3 skill points. To make sure you have to spread them, it removes Navigation and spreads its per-level bonuses to level5/10 bonuses spread around lots of other skills.
At the very least, you could merge Fleet Management into Command Experience, merge the two diplomacy skills, merge Fleet Deployment and Station Industry, and place it all under leadership.
P.S. Loltrino rebel stompfleets wut wut