My general rule of thumb has been to base defensive upgrades on the rest of my fleet. If I have a strong squad wing, then I probably aren't as afraid of enemy squads blowing up my big ships. I can probably safely take ECMs to defend against single huge hits from enemy ships. If I don't have much of a squad wing and enemy bombers are scarier, then EWS can really shut them down. (Or at least delay. Toss your squads hugging each side of your ship and put flak out the front)

Then if I'm running Motti, I take RBDs for comical amounts of HP.