Each deflector type enhances certain properties of various Bridge Officer and Captain skills that you get. If you right click on the deflector and choose "Info" it will give you a full rundown on what each stat is and what that stat affects. That way you can choose which deflector you want based on the skills that you have.
To amplify on that a little, there are a set of attributes that are available to all deflectors (wiki link). Each of the deflector types have some of these attributes inherently (another wiki link), and then they can all have some of the attributes as additional properties.
Simple example, the Positron Deflector Array has inherent attributes for Shield System (hit-points), Shield Emitters (regen), and Structural Integrity Field (hull hit-points), so it is a very good deflector for a tanky ship. Find a deflector with "[ShdS] [Em] [SIF]" attributes, and you'll get that same set of boosts. Find a Positron array with those attributes and you'll get the boosts twice (first from the inherent, and again from the additional attributes).
Basically you need to look at the available attribues, find the ones that match with your specific playstyle for each ship, and then find an array type and attributes that deliver on what you want.