Well, I don't think there are too many 'fail-worthy' skills. Care to provide some examples?
High level, I'm really only familiar with the Engineering ones. Some are clearly better than others, but it could be a lot worse. I would agree that some are too situational (Beam Overload, or Warp Plasma come to mind), but generally speaking, I'm seeing a pretty wide range of abilities chosen in game.
(I'm assuming you're not talking about 'player' skills from the skill tree, if I'm misinterpreting, my bad.)
Has anyone noticed that there are only 2, maybe 3 Commander level Engineering BO space skills available from the trainer? One of them is Aceton Field II. Seriously, there needs to be more.
I'm assuming this is an attempt to increase the value of rare BOs with high level abilities.
It is kind of annoying, but it's similar to how gear is treated in many games - you don't buy they best stuff in the game, you have to work for it... which usually means killing something over and over and over, but the merits (and drawbacks) of that system warrants an entirely different discussion.
STO is kind of different, in that so much above average gear is available via exploration and FOR FREE. Why anyone would ever buy odd leveled white weapons from the exchange is beyond me...
There are very few skills for all the high level BO skills. Because you have to find other BO's that you find or purchase to train them... Or the other option is to train them yourself. Almost all the skills you can learn in the Captains skill tree give you the ability to train the highest rank of a skill associated with it.