In a nutshell, I propose to swap Boarding Party from Engineering with Target Subsystem abilities from Tactical. Furthermore, I would upgrade the Target Subystem abiliteis from tier-1 ensign through tier-3 lt. commander, to tier-1 lieutenant through tier-3 commander. The reasons for this are detailed below.
First, engineering has the fewest number of commander-level damage-oriented BOFF abilities. Of the 13 engineering abilities available, only 4 of them are commander-level damage-oriented abilities (aceton beam modifier, boarding party, directed energy modulation, and eject warp plasma). Meanwhile, tactical has 16 total and 6 are commander-level damage-abilities (none of which are Target Subsystems). This proposal would give engineering 16 total and 7 commander-level damage abilities, and tactical would have 17 total and 7 commander-level damage abilities (one of which would be Boarding Party 3). Science would still have more than either of them, with 18 total, and 9 commander-level damage abilities. So, first thing, it would smooth out the ability distribution a bit.
Second, it makes little sense for Boarding Party to be an Engineering ability, since its more about Marines taking over a ship than anything else, and it belongs with the anti-BP function of Tactical Team, since they are both about shooting in the hallways and subsystem control points. In fact, I would like to see BP and TT get an effectiveness buff from one of the Tactical ground skill pools, something like Combat Specialist, as a general base for the Marines effectiveness.
In the same way, it makes more sense for Engineering to have the Subystem Targeting abilities. "If we shoot this emitter array here, their weapon power will collapse" is something you expect to hear from Geordi, not a redshirt.
It would also give Engineering some control abilities other than Eject Warp Plasma, and would especially make cruisers much more effective at control due to the large number of high-level engineering BOFF slots. Science-oriented cruisers and carriers with high-level engineering become a lot more interesting and potentially effective if they are able to target engines and shields effectively

Implementation issues arent that signifcant. Sscience ships would need their inherent subsystem targeting edited a little, maybe a couple of DOFFs changed a little, nothing else really.
Comments
Did you divide by 0?
Mess with logic?
Move me to an alt time line?
I never see good ideas posted on these forums, it's all selfish cry baby posts with a touch of Cryptic hate mixed in for flavor..... why did you have to go and break the internet and make sense
I have a headache... I think I will go lay down for a month or two
(All jokes aside, yes I do like the idea and second it)