IMHO, phasers are good until endgame. Their ability to shutdown systems seems to work most of the time for my characters. A simple setup with phasers and photon or quantum torps will work well in PvE. Having said that though, I give my characters other weapons based on their profession as they advance: Engineers get plasma beams/plasma torps, Science offficers get Tetryon beams/transphasic torps and Tactical get phaser or Antiproton cannons/quantum torps. .