I find it better if you think of missiles of a supporting weapon rather than a main alternative to the energy/kinetic. In such a role, they work awesomely.
I tend to run more of a fighter based fleet, rather than larger ships. As a result, PD is always an issue. However... Often I find those fighters cause the enemy ship to make a choice... Shield against my weapons fire, or shield against the fighters shooting it in the backside. Same thing works quite well for missiles. Sure, it might block the missiles, meanwhile my energy weapons are tearing a hole on the other side. And vice versa. It also works to have missiles coming at them from multiple angles. If you can get behind that onslaught, and fire a few MRMs while your support missile ship fires a few Pilums into his front, than he has to make a pretty crappy choice of what is going to eat him first.
You can also actually block PD with your shield! Just basically ram them while the pilums follow you in...
Missiles are a VERY situation weapon. Using them correctly is key. Sure that energy cannon does decent damage... But some MRMs at near point blank range on a venting/overloaded target does much, much more.
Also, I find missiles are extremely good for killing freighters and their converted counterparts, (destroyer level) as they generally have no shields/weak shields. A nice dose of MRM makes that mule go down nice and easy with a Frigate.