It's an interesting idea, but I think even more complicated than it has to be.
Simply make it so that you ship stats are determined by captain class, ship class, and rank and then make all BO slots universal in the cmdr, ltc, lt, lt, ens layout.
They could even through in the XO mechanic they've been talking about forever to add a little variety. You'd then have four variables that determine ship's "stats" with a lot of different skins flying around.
I also think they should make the special consoles class specific, but whatever.
I like the idea of all BO ship slots being universal. Let the player decide how he wants to run his ship. However, consoles would be dependent on a relative BO being present. You could not equip a Sci console unless you had a least one Sci BO on the bridge. (You could put a universal console there though.) Would make for some interesting builds...
Sounds good in theory, but players would abuse it to no end I fear.
A player, regardless of PvP or PvE, will always want to have the single most overpowered build possible.
And at the moment that would mean, go, pack as much DPS as possible.
Nearly Every ship would run Commander and LC tac slots, at least one Lt tac, and the rest be engis for survivability.
Some players would build zombie tanks like never seen before.
And don't let me start on the monster sci ships this would make possible. (although only the min/maxers wouldrealize this).
Spell casting inflation would go through the roof... And the game would stop being fun.
WIth all those +1 consoles it already has stopped being fun to some degree.
I have stopped dabbling in PvP for a reason...
To have such one sided builds is bad game design.
The challenge is to overcome the limitations your ship has and utilize the perceived disadvantages.