Has anyone else noticed the issue with Starship Command and the following skills, being that the Commander and Captain ranks are dead-end skill point sinks? I will illustrate by example, assuming a Science Officer. It should be obvious how it would work the same way for whichever ship class you prefer.
1. As a Lieutenant, you can get Starship Command, which improves the function of any starship. Useful skill.
2. As a Lt. Commander, you presumably pick a type of ship. In my case, this was a science vessel. I take Science Vessel Captain, which improves the function of any and all science vessels on top of my bonus from Lieutenant.
3. At Commander, it falls apart. You can take Research Science Vessel Captain, which applies a bonus to research science vessels only. We see the problem as soon as we get promoted...
4. As a Captain, you get a long range science vessel and access to the Long Range Science Vessel Captain skill. This adds to your Starship Command and Science Vessel Captain skills, but any ranks you put in Research Science Vessel Captain have no effect because this is a different type of ship. So basically, any points you put into the captain skill at Commander are completely wasted.
5. You hit Admiral and the problem repeats itself. Any skill points you spent for being the captain of a long range science vessel have no impact on your choice of Admiral-level science vessel.
As designed, it seems as if you should skip your specific starship command skills at Commander and Captain, unless you want to rely on a respec at Admiral? That seems like a poor design.