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I've got a small box which I keep on a night stand next to my computer. In that box are little slips of paper and written on them are questions about STO which I haven't yet figured out. On today's slip of paper is this question: Why can't an Officer Candidate who knows a II level skill teach that skill to a BOff who has the same skill but at level I? I find that the BOff of lesser skill must give up something other than the skill I'm interested in improving in order to gain the higher level skill. I'm sure That it's possible, with some effort, to do what must be done in order to gain specific higher skills for a BOff but why does it have to be so difficult? I'd rather not end up with a BOff with two levels of the same skill 
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For example Emergency Power to Shields I is an Ensign ability. Emergency Power to Shields II is a Lieutenant ability. This means that II must go into the Lieutenant slot so any ability currently there must be removed.
The reason this is done is to force you to strategize. If the rank II ability isn't really needed then you should just keep the rank I. Continuing with my example maybe the skill that will get removed due to Emergency Power to Shields II isn't needed as a rank II ability so you can just get it as a rank I ability.
Just keep in mind that Ensign doesn't always equal I of a skill, Lieutenant doesn't always equal II of a skill, etc. There are only 3 levels of each and they can start at Ensign, Lieutenant, or Lt. Commander.
There's no way of having someone with Skill level 2 teach level 1 to someone else. They can only teach the skill they already have. It won't duplicate anything since when you do training like that, that BoFF will NOT join your crew. They are discarded at that point (I guess sucked out an airlock or something)
I know all this. I guess I haven't been clear about what I'd like to do with my BOffs. What I'd truly like to do is promote my Ensign to Lt. and increase his level 1 skill to a level 2 skill by having some NPC or my Captain teach him the higher level skill. I'm not the only one who puts at least a little care and emotion into developing BOffs. It's just a shame to turn them over and discharge after all the time and energy spent making them look just right, spending EC on uniforms and just working with them as characters. Consider how we as fans have opinions about any or all of the characters from the various iterations of Star Trek. I like my BOffs and would like to see them develop into characters with the same appeal as any of the other Star Trek characters I like. When my Ensign Moon is promoted, I want her ability to do whatever at skill level 1 also to be ungraded with training. Of course I'm assuming a level 2 skill is more efficient and or effective than the same skill at level 1.
Have you looked for the BOff Trainer NPC ("Power Store") on SB01? He can train most level I and II powers for Merits. (He's in Personnel -- 2 O'clock on the map -- near Sickbay. KDF counterpart is in the Combat Training room on Qo'noS.)
Anyway you cannot increase a level 1 skill to a level 2 skill. That's now how the game was designed and the game will not change. If you really want the level 2 version of that skill you need to sacrifice another one. Then you can replace the level 1 with something else that goes into that rank slot.
If everyone could increase the level of all their skills to level 3 then everyone could have the best of everything. That's not how the game was designed. You have to make sacrifices and compromises with your skills. Its all part of building your character and perfecting it.
No one is telling you that you need to get rid of your BO. If you have a BO candidate with skill XYZ that is level II then you can train it to your BO. However if XYZ is a Lt. Commander skill then it'll train your BO in that Lt. Commander skill. You cannot train that skill into the Lieutenant skill.
Honestly right now I'm not sure if you are making a request that skills should be upgradeable or if you have a question as to way they aren't.
For future reference, please separate your long paragraphs, it makes it easier to read. Thanks.
Heezdedjim, you're very close to giving me a satisfactory answer to what I perceived as a dilemma. Thank you for giving my post some attention and actually thinking about an answer. It seems a bother to have a BOff with EPtS I & II in the same skill. I was trying to avoid that. Having a shorter cool-down is an advantage but it was my impression that a higher level skill provided that advantage. To my mind, it makes sense that attaining a the higher level in a skill would represents a certain mastery of the skill.
I understand that a Captain who learns all nine ranks of a skill can train BOffs to level III (3) of the skill in question. It seems to me that this is exactly what I want to do with my Ensign whom I have promoted to Lieutenant. You do say that the Captains skill rating matters more than the skill rating of the BOff but you seem to contradict this when you say (parenthetically) "higher skill are generally better than lower ones."
All said and done, I think this game needs a well written manual which covers all these little questions about the game. Some people have taken upon themselves to put a great deal of good STO information in one place. My hat is off to them. I guess I'm just old fashioned enough to need a hard copy manual with an index, glossary and killer illustrations.
Thanks again Heezdedjim. You were most helpful.
Each BO has 4 abilities based on his/her rank. Ensign, Lieutenant, Lieutenant Commander, and Commander.
Each skill can only be assigned to a particular rank. For example, Emergency power to shields II will ALWAYS be a lieutenant skill. EPtS III will always be a Lt.Cmdr skill. You cannot have EPtS III in an ensign ability slot.
Generally speaking, the higher the skill level, the more powerful the ability. For example, EPtS III will heal your shields more than EPtS I.
When training a BO with another BO, the new skill will replace the old skill in the same rank. So if you use a candidate with EPtS III to train one of your BO's, the EPtS III ability will replace whatever skill is in the Lt.Cmdr slot of your current BO. If your BO happens to have EPtS I, that skill will not be affected, and will remain as an ensign ability for your BO. The result will be that your BO will have both EPtS I ensign ability, AND EPtS III LtCmdr ability.
For some abilities, it may be advantageous to have 2 copies because of shorter cooldowns on the second copy.
Yup. But either the OP didn't understand what everyone was saying, or everyone wasn't understanding what the OP's question was. So, I've put it in another way.
Exactly.
/10char
Can "special" BOff's be trained by other people? For example, I have the Holographic BOff, and I would like him to have MTIII. One of my fleet members can train that ability, can I give him my Holo BOff to train it, or is that Holo BOff strictly locked to my account?
The real solution to this problem would be a special "tradeskilling" slot in the trade window which you could place any item, bound or not, into for another player to work on. They would then be able to "see" and work on it, but would never get possession of it. This would solve both the problem of trade skilling or training unique and bound items or crew, as well as remove the possibility for scamming which exists where you have to trade something away to get it worked on. Other games do something like this, but so far STO does not.
Latinumbar, others may think they've presented an answer to my question but your clarity and brevity put them to shame. You've stated clearly what should have been written in a STO manual about BOff Training but isn't. Your post, on this subject should be a sticky. All praise to Latinumbar. You are a God.