I just got done running a series of tests and all resulted in the same thing: MPA sucks. All the following were done with all research in a VR vs VR mirror and no micro whatsoever at a star (increases AM regen and reduces hull regen).
I tried 1v1 Skirantra with MPA vs Skirantra with no abilities and same SC configuration (all bombers). They died within a second of each other, inferring that MPA had no real effect on the damage output of the SC involved.
Next, I tried other fighter configurations. If fighters exist, it will slightly help out the bombers. Very slightly. The two Skirantras were only separated by a couple hundred health points. Enough to not blame phase missile chance, but not enough to make it considered helpful. After all, the enemy ship didn't have any ability so winning by a tiny margin says something about how weak this is. I tried various SC configurations with low level Skirantras and all resulted in low margins of survival for the one with MPA against the enemy mirror Skirantra whenever fighters were involved. This is presumably because there was something shooting at them. MPA appears to do nothing to damage output and instead focus on durability.
Then, I tried some more realistic situations. I knew that RC would overpower either of the other abilities so I figured I'd try one Skirantra with level 4 RC & MPA while the other has level 4 RC & SB. Neither one had Replicate Forces (not that it would have mattered as it was a 1v1). Scramble Bombers quickly allowed the Skirantra with it to gain air superiority and took down the Skirantra with MPA easily, only suffering about 15% hull and 35% shield.
Last, I hoped that MPA might be saved when dealing with fleets, so I pitted new Skirantras with the above characteristics against each other, each one escorted by 3 LF, 5 LRF, and 5 flak. Because of happenstance, the MPA Skirantra's escort was in a slightly better position than the Scramble Bombers Skirantra's. It didn't matter. Once again, Scramble Bombers demolished the Skirantra with MPA and the result was a total loss for the MPA side. No ships on the SB side were killed.
So to summarize, don't ever get MPA.