My take is that when you are sufficiently experienced with the game's bridge officer abilities, these bridge officer abilities become the primary form of defense and item sets play a lesser role in your ship's defenses. As a result, I tend to prefer using item sets for offensive advantage rather than only considering defense when it comes to picking my item set.
Don't get me wrong, a strong shield is still important but there are other ways of getting a strong shield (eg, consoles).