Here's an idea for both increasing the value of current Tier 5 starships, as well as giving the new 'Refit' starships a suitable niche and 'hook' for players that prefer to purchase the new ships.
For existing Tier 5 ships, increase their 'off-spec' BOff slots from 1 Ens, 1 Lt, to a single LtC.
Assault Cruiser: 1 x Comm Eng, 1 x Lt Com Eng, 1 x Lt Sci, 1 x Lt Com Tac
Star Cruiser: 1 x Comm Eng, 1 x Lt Com Eng, 1 x Lt Com Sci, 1 x Lt Tac
This would keep the number of powers that the ships have at VA1 the same, while opening a much wider range of powers to Captains of differing careers than the "optimal" ones for specific ship-types (Eng/Cru, Tac/Esc, Sci/Sci). Take an Assault Cruiser, for example, a Tactical Captain in such a vessel is restricted from many of his best powers, due to the limited number (and rank) of Tactical BOff-slots, while simultaneously being hindered from optimal Engineer BOff's because of his inability to train BOff's in the higher-ranked Engineering powers. While the advent of Season Two and BOff-trading will mitigate this somewhat, an arrangement of BOff stations like this would allow much greater flexibility and diversity in ship designs, particularly for those "off"-combinations.
For the BOff layouts on the new, 'Refit' starships, instead of adding an Ensign slot in the "matching" career slot of the ship type (i.e. The Defiant gets an extra Tac Ens, the Excelsior gets an extra Eng Ens, etc.), why not give them a Universal Ensign slot? Again, diversity and choice lead to a happier player-base, and, since it's only an Ensign slot, would not be game-breaking, and, would compensate better for the losses suffered elsewhere in exchange for the ship-specific abilities (ablative armor, cloaking, etc.) that are equipped on the Refits.