When I design the defensive doctrine of my ships, I tend to go for a layered approach, stacking on as many different systems as is feasible. for example, I use armour, shields, CIWS, pd, flares, and 2 kinds of AMM (one for getting rid of decoys and one with retargeting meant for missiles) all together to create a 'layered' defense. I am not sure if this is meta/optimal, but I think it's cool so I do it for RP purposes.
Anyway, I was curious about how everyone else handles their defense doctrine, as I feel like their are many threads about individual defensive systems, but not many about how they fit together.