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.
Missile:
it doesnt do damange to enemy Battleship's shield..or sometime even Cruiser's..give it a bigger explosion radius would fix the problem..and longer range..a little higher speed.(110m/s)..and maybe change the effect to some bigger explosion effect would be cool (use the effect from Mines, i remember one of the effect is a boom then there is a "ring" around it)..and maybe decrease enemy usage to 70~80% of its original
Flaks:
give flak a longer range, so big ships can actually use them and hurt the fighters..and a little higher damage..the flaks takes 10% of fighter's shield each hit..too small..maybe 20~30% would be great..