I think science, engineering, and tactical teams should come to each captain free and not take up a bridge officers slots. In the movies and tv shows these teams are already on board and at work.
Also I would like to see a universal console cloaking device for the Fed side.:
The engineering teams in the shows are more like the passive regeneration of your hull, always working in the background to maintain the ship whereas the team skills that your BOs use are more like damage control parties, ordered to severely damaged areas when they're needed.
I have to admit I don't like the idea of them being free to each captain class, as it stands there's an opportunity cost in each skill, to take one you have to not take something else. Giving everyone everything is just too easy and dilutes the game IMO.
Cloaks are for the KDF, although not all KDF ships pay for the cloak (Negh'var) most pay a penalty, usually in Hull and Shield strength. The Vor'cha for example is the KDF equivalent of the Sovereign (based on BO and console layout) yet has 3000HP less hull. If the Federation got a cloak then it would also have to take a reduction in hull and shield strength to compensate.
There's also the problem of making the factions too similar, they're already very similar but adding cloak to the Federation line up would make both sides almost identical if not for the UI. If you really want a cloaking cruiser, then roll a Klingon if you haven't already (not being sarcastic, it's a genuine suggestion). The cloak isn't actually all that useful other than the approach, although the extra manoeuvrability of KDF ships makes them a lot of fun anyway.