For starters, dump the bio-function monitor console as it's pretty useless. Since a gameplay update in either season 1 or season 2, crew is only useful for repairing your ship out of combat (in combat you'll hardly notice the very small hull regen). I suggest replacing it with the borg console (gotten via the "Assimilation" mission).
Next, get rid of the transphasics and replace them with quantums or photons. Until Cryptic really buff them, transphasics are rather pathetic in comparison to them.
Stick a field generator Mk XI console in an engineering console slot, which with give you 35% more shield capacity (not these consoles will not stack).
If you're going to mix beam types, I suggest you use "directed energy distribution manifold" instead of "phaser relay" consoles as they effect all beam weapons (but only beam weapons).
The BO powers I'll leave to later, but I think you should promote your engineers. :P