About the so-called "point defence" (secondaries);
Against fighters, its meant to act as supression fire. This means that it keeps the fighters and bombers that are targetted on their toes, without doing much damage to them unless they make a mistake. You are meant to have escorts to do the real damage to the small guys. If battleships were to effectively counter fighters and bombers, then everyone would have a capital ship.
About the missiles;
They are meant to target cruisers and battleships. Maybe they should be renamed to "ballistic missiles", because that's what they really are now. They may seem inefficient for the damage they do, and are fairly easy to shoot down for an enemy fighter paying attention. However, they are meant to disarm enemy capital ships (cruisers, battlecruisers and battleships). They are also very useful for blowing off the turrets on docking rings (or so I saw during the closed beta anyway).
About the flak;
These are meant only to act as a deterrant to fighters and bombers when they get in close. Its very hard to make flaks "better" without making them stupidly good as they were in 4.83. Those with a longer memory of 4.83 will know that cruiser flaks on a Kusari destroyer raped fighters SO hard, it wasn't even funny. Me, 5 seconds, boom. Hilarious, I know, but its not good to return to that.
Get a grip people, and relearn how to use your weapons, and what roles they now fill. Things change; I learnt that a long time ago. You should too.