Phasing through shields. Wow, it sounds powerful doesn't it? But 99% of the time its useless.
Against TEC or Vasari? Pretty much always useless, both rely on their armor more than anything. A simple damage boost to phase torps with upgrades would be better all of the time, like other races can research for LRM.
Even against Advent they are usually useless. Until you get a very high percentage of phase penetration, their ability is useless. Ships always die after their shields are down from other fire sources (Which means phasing didn't help at all, they only help if the ship dies with shields up). In fact, phasing often increases the time it takes a ship to die, as when you are damaging armor and shields, it lets the ship take advantage of armor and shield regen, extending the life slightly.
The ONLY time they are useful is when you
A) Have pretty much only LRMs

Have fully upgraded phasing
C) Are trying to kill a Radiance or something that is being shield regened and mitigation boosted.
The rest of the time the ability is pointless. And having it at low levels is ALWAYS pointless. The above conditions happen very rarely.
I have a simple suggestion to fix them. Change the upgrade path to giving a damage boost, like every other weapon upgrade path. Then add a couple techs at tier 6 or so, which give a big boot to phasing. Have them take the phasing almost to where it is now with full upgrades, but not quite because of the damage boost. Thus, LRM upgrades become useful the rest of the time, and phasing is still in play, and balanced.
Another thought is to make it so that when the phase chance goes off, it does damage to both shields and armor (so if shields are up, it has a small chance to do double damage basically). It would still do less overall damage than a simple upgrade of damage at 5% a level, since shields aren't always up, but would maintain the flavor of the torps.
Right now the phasing tech line is never researched unless you come across the rare combination listed above, at which point you research the whole thing. Make it more universally useful at various levels of tech upgrades.