Just to make sure I understand the question right...
Are you asking about captain skills (ie, your own) or about bridge officer powers?
Captain skills aren't limited by stations - so even in a cruiser, you'll still have access to all of them.
Bridge officer powers are limited by stations - so in space, you would only have access to a maximum of a lieutenant commander bridge officer power. However, on the ground, your bridge officers can use any and all abilities they have.
I do agree that the stations on higher tier ships are a bit too restrictive. It doesn't make sense that one should have to fly an escort to make use of a commander-level tactical bridge officer power. I can understand the point of limiting the stations, however I think that from tier 3 and higher they should probably all get bumped up a little - ie, ensign stations should become lieutenant, and so on. This topic probably deserves an entire thread devoted to it to give the devs good feedback.
So yeah, as far as the bridge officers go, definitely an issue, and here's hoping the devs address it before we're all wondering why we bothered to promote those bridge officers.
Yes, I will have availability to these powers that I have as Captain - BUT I will not be able to give my L3 skills or use them with any BOF's. So the advantages of having a cruiser (more tankage) is severely offset by only allowing a L2 Tactical BOF in this hybrid setup.
The only L3 skills I can use are my own, and from level 20 through end of game my Tactical BO's have the same skill (unless replaced - so more accurately ONLY a L2 skill for the rest of the game).
Perhaps by design - or can a RARE L2 BOF *ever* have a L3 skill? (super rare?)