The thought I had about it - and it's not fully fleshed out, and I'm not fully committed to doing this, so, big disclaimer/grain of salt - is to change SO to function as an active ability instead of a constant passive buff.
The idea being that yeah, if you nerf it, it gets less interesting. But as is it's also not all that interesting because - alright, it does add a playstyle, but that playstyle is very similar for everything and there's not too much to it. If you make it an ability where activating it, say, costs the ship some peak time (and then CR when it's out of PPT) then you can have it be really powerful, and "when do you trigger it" becomes an interesting tactical decision. (What effects exactly it would have is up in the air; in a similar vein to what it currently does, though.)
And then you'd have a new control for "active ability"; something like Neural Transfer would use that control, too, ships would be restricted to just one hullmod that adds an ability (and the door would be open to more abilities like this that can be slotted into ships), etc.
Again, though, this is all fairly half baked; these are just my thoughts at the moment. It's entirely possible none of that would go anywhere. (And if it did, I'd probably leave the original SO in the game and accessible via console...)