It seems the set bonus is not that much great... I wonder if I should keep them or not
Tho 25% faster cool down is nice to have!
How great it is depends on what ship you're using and where you have them slotted. If you're not building to Science you can easily put 2, or all 3, of them in the Sci slots and not really lose anything.
It' a bad idea to equip all three enhanced engineering systems consoles. Engineering could at minimum have neutronium alloy which yields far more survivability. Tactical should surely be reserved for damage + consoles. Leaving, as the prior poster noted, science consoles. One of the science consoles has to be a field generator...40% shield (35% in the cheap seats) is simply too much capacity to overlook. Leaving at most two consoles that could be used for enhanced engineering systems. Then you have to decide if you can forego + 15% shield regeneration and +3.5% or more shield power...a very tough sell.
It' a bad idea to equip all three enhanced engineering systems consoles.
It depends on whether or not you plan to use all three console powers. If you're going to use them anyway, then the bonus is nice, but it isn't really worth mounting them just for the set bonus if you have no use for the console power.