No idea. Why? Because such things have not been made clear yet. Hopefully soon we will be given the toolset to make educated decisions on such things. Doesn't need to be complicated. We all know 50% > 35% and 230 DPS > 213 DPS...
But yes, there is some serious lacking of information to determine which is the better item and why and under what situations.
Some bridge officer powers receive a buff from the different systems. In the tooltip in their skills view, it says which system - but it doesn't say when mousing over the power in your tray. I had to choose between dish and field for that yesterday myself for tachyon beam. (And now i can't remember which it was without logging back in to the game.)
But yes, which powers you're using is what should inform your choice.
It's going to affect some of your science space abilities.
When you look at a science skill, it'll tell you what system it uses. If you boost that system with consoles and your deflector dish, it'll improve that ability. Click on the power in the skills window of your science bridge officer, and it'll tell you what subsystem it uses over on the right. If a console you're using is boosting a system that none of your science powers use, then it's essentially going to waste.
Example, the only science power I'm currently using is jam targeting sensors, which uses the sensor subsystem. Therefore, I make sure I have a deflector dish and a science console that boosts sensors.
Some of the system names sound similar, so it pays to pay attention.