Like many, I like to use a range of skills, but my attacks focus mainly on 2 or 3. In my case, HY, Beam Overload, and sometimes Fire at Will. When I promote my BOs, however, it's very difficult to do the obvious--go from Beam Overload II to III, for example. I often have to give up another power I already have and want. As a result, promotion means turning my tactics and powers upside down--very annoying when I've invested skill points in a skill that I now can't have until my next rank, if ever.
This makes no sense. Essentially, in battle, my commander replaces an ensign who just got killed, let's say. But the computer says, "sorry, you can't fire Beam Overload I, even though you used to have it and now have Beam Overload III. Have a nice day." It just doesn't make sense--stations don't have rank, on Earth or in space. Officers have rank and the skills should follow them. At a minimum, of the powers I must lose in order to simply go from HY I to HY II, for example, the next rank up from a power I have should be an option. New powers should be based on an officer's rank, not some odd notion that a chair and a computer on a bridge don't work any more because you got promoted.
I'm now at the point where I avoid promoting BOs because of the chaos it brings to my powers and preferred tactics. For all that is holy, developers, please address this. Easily going from Power X I to Power X II should be really simple. If my BO knows I, II should not be hard. We've embraced the notion of aliens with lobsters growing out of their skulls, but a commander not being able to fire a torpedo anymore without reprogramming the ship is just too radical? The power tree was poorly explained, but actually makes some sense when you figure it out. The training/power replacement system, however, is complicated and gets in the way of one goal of the game--allowing players to adjust their powers to their play style.
Please consider changing this. I'm not the only one who is driven mad by this illogical system.