Also, remember phase missiles take some time to research. The other weapon upgrades for the vasari capital ships appear later on in the research tree; while Advent have their laser and beam upgrades for caps early on. Phase missiles is all that the vasari caps have, to start with...
This is not quite true... Phase missiles are way cheaper and faster to research for the benefits they give than the Advent weapons upgrades : First, most Advent caps have their damage divided between laser, beam, and plasma. So if you want to completely upgrade their weapons, you have to research the three. Lasers are cheap, I agree. Plasma is a bit more expensive, and also a bit more expensive than phase missiles. Beams, the thing you generally want to upgrade when you have illums and bombers, start on tier 3, while phase missile tech starts on tier 1, which make beams far more expensive...
With one upgrade sequence you upgrade assaillants, fighters and bombers...
I didn't think these missiles were so powerful before I read the post from Pbhead about them. Also, the simple fact that fully upgraded phase missiles make vasari fighters better than heavy cruisers at taking out cap ships is just... Plain wrong... Why build enforcers then ?...
However, as you and Darvin said, if you remove the shield mitigation bypass, they become totally useless (exception for taking out guardians probably), unless you change shield negation chance to 60 or 70%... I personally favor a higher research cost, maybe tweaking the order, get damage increase first, then shield negation, or a more combined path, getting damage and negation at each step, I don't know...
Concerning bombers, the fact that flak is not very good at taking them out is a bit counter-intuitive to me... In real life, flaks are way more effective against bombers than they are against fighters, because bombers are slower, less manoeuverable, thus easier to track... It's a game, there's no problem to me about that, but maybe a combination of increasing fighter durability, flak efficiency against bombers, lowering bomber efficiency against what they're not meant to take down would be enough, and would bring more heavies into battle... I don't really know what I think about the tether idea, it would be a big change...