Heh, this again
IMO:
Phased weapons should be slightly weaker than the nearest comparable standard weapon.
Phased shields should be available early, with only a bit more research than normal shields.
Phased shields should also be slightly weaker than standard shields.
Then, phased weapons become a support weapon instead of a main gun:
By carrying a few phased weapons, you may force the enemy to use the weaker phased shield generators, and take advantage by bLasting away with your more powerful normal damage weapons.
You may not even need to have any phased weapons in your assault fleet, but if your opponent believes you do, he will have some decisions to make. Psychological warfare anybody?