Why do TEC get repair bays that are 267% better than Advent or Vasari repair bays? 40 hull per second? Thats astounding! I can understand why Vasari bays might be gimped (Repair Cloud ability from the carrier = mobile repair bay for everthing in range) but AFAIK the Advent really get shafted here.
Because TEC are generally weaker on shields, so they get better repair abilities. The Advent get some very good shield management and have better shields in general, so they get weaker repair 
When a phase missile phases, it not only ignores shield mitigation and shields but does it also ignore armor?
I don't believe it ignores armor.
