Commentary:
1) I have been thinking that ACD Phantoms would have been much better balanced if Advanced Cloaking Device simply had the following text at the end:
"Then receive 1 stress token."
Think about it for a minute then let it settle in - I'm pretty sure that would reduce the effectiveness of the Phantoms. You would at least know that they are almost certainly going to perform a green maneuver next turn. You can build around this by adding Captain Yorr or Wingman EPT, but this would encourage more build diversity and would be a good thing.
Edit: I would also be OK with a cost increase. 4 points is probably not enough.
2) YT-1300 + Gunner + Z-95 support I'm not as worried about being permanently dominant, unless it HAS to stay as a counter to ACD Phantoms. It's a great list but is very beatable, especially by a swarm (either faction), if you focus down the Falcon first.
Having flown the Phantom through 6 rounds to a top 4, I can honestly say that it is a ship that is very susceptible to fatigue and the vagaries of the dice. At the end of 12 hours (including a half hour for lunch and a half hour for supper), I was having a hard time making optimal decisions. Added to that, cold evade dice can really hurt a Phantom player - in my case, on two separate shots I rolled all blanks with a focus in hand. This takes nothing away from my opponent mind - he gave himself the opportunity, and although we've played the matchup repeatedly, sooner or later he was going to get me.
Regarding the YTs, I think Spokane demonstrated that there is a consequence to relying on them as a counter to Phantoms - there were quite a few that showed up - but there were a lot of lists designed to destroy them in attendance and they got frozen out as a result.
Don't know if it helps you at all, but the two 5-0 lists at the end of the Swiss were the top 4 and top 8 phantom builds. I played the ultimate winner in the fifth round and beat him in the mirror lol.