I could see the need for a new set of slots for universal consoles, like the Odyssey class, if you bought the 3 pack to get all 3 versions of it maybe you did because you want to get the most out of that ship by putting all three consoles on 1 ship but to do that you have to sacrifice something since those consoles only go in either a tactical, engineering, or science slot.
My suggestion would be instead of universal slots just designate consoles like that as miscellaneous and add 3 miscellaneous console slots to each ship that uses those special ability consoles. It wouldn't have to make the game unbalanced because they could do something similar to what they did with the Odyssey, just let you use 1 special skill at a time. With that ship if you have all 3 consoles you can sepperate the saucer but you can't launch the Aquarius escort or worker bees until you dock the saucer with the drive section.
When it comes to universal consoles, I would say the Assimilated Module or ZPM actually work rather well as 'universal' because they have passive, always on bonuses that you are trading for other passive, always on bonuses. it gets mucked up when you have the standard Universal consoles that are really just additional spells, that many have a very long cooldown.
Imagine say, the Red Matter Capacitor, which is a very popular device, imagine how many would use it if it was a console instead? The CD is too long, the effect is nice, but the CD means it is not always on. In the cast of most uni consoles having to trade a possibly useful CD for an always on bonus is a hard thing to deal with, and generally feels bad. Making the CD uni's into devices would be nice, especially since they provide no passive stats.