Other than one single occurrence in Psion, I believe discipline only exists in High Guard. In Psion, there is no description of what the skill is.
Gripe 1 - I think that any skill not used in the Core Rules should be described in detail in any publication it is used. For example: Instruction skill originated in Book 2: Mercenary and is described there but it also is in Book 2: High Guard and Book 3: Scouts without any description of what it is or even a reference to what publication the description does occur in.
Gripe 2 - Why is it that an Agent or Merchant or Psion is incapable of Instruction and pretty much only a Navy character has discipline!?
Gripe 3 - These new skills are a bit broken.
Discipline: What do you do with Discipline 0?
Discipline is usually used only in campaigns where the characters are still in the navy
Discipline can be gained several times in skill tables and events. What does a character with discipline do if they leave the Navy?
Instruction: Compared to training via the Core Rulebook, an instructor only cuts the length of training a few days but now there is a skill check to succeed. No details are given for retrying; Does the character start all over from the beginning? And what does "depending on Timing" mean?
It's interesting that the newer books like Agent, Merchant Prince, and Dilettante didn't incorporate the new skills found in other books. The Interrogation skill seams like a good fit for Book 5: Agent. Other than being an unnecessary skill since it can easily be covered by Persuasion and Deception, it seamed well described without glaring flaws.
[/End Gripes]
For these new skills you may need to make a decision. If you like a new skill, I believe you need to find a way to duplicate them in the other careers so that characters are balanced and compatible. If you don't like a new skill, you can replace them where they show up with another skill well suited to the career.
Personally, I don't care for additional skills. The work trying to integrate it through all the prior and future publications isn't worth it. As pointed out recently by someone in another thread (possibly Icosahedron? sorry if I have the reference wrong) you can easily role play based on the career and a more limited set of skills. A marine with several terms who rose in the ranks to squad leader and platoon leader should have some leadership, admin, and instruction skill whether it shows up on a character sheet or not. The more skills in the game, the more you feel like something can't be done unless you have the skill.