I really would have liked to have seen greate specialisation in the character generation. In particular at some point in the advancement path I would have liekd to see a choice being made about specialist training where you make a choice about a new skill tree. These dont have to be massive bonusses and couldbe as simple as allowing you to increase certain existing skill groups beyond 9 ranks. A great way to add this would be by including the 'missing' ranks from the tree, such as Commodore and Lt. (JG) Examples might include:
Training for specific ship types - using existing 'classes' escort/science/cruisers
Specialisation on ground or space
Specialisation within the classes (medical of A.N.Other scince or gunneryVs tactics etc)
Specialisation within existing skill sets (repeat of some class skills allowing the skill to be incerased beyind existing maximum)
What I would be hoping to improve in the skills this way would be a move towards the development of a career rather than the bland tree we have now. Ideally showing a progression that starts with starflet academy moving through various schools of training. This could become incredibly flexible allowing easy additions of new skill sets for new races and development options. It also allows a greater diversification of characters moving away from the very limited class option.