I figured I would compile a few strategies various people use to go against a Phantom and win. Some of these will be totally obvious, while others will hopefully make you go "Ahh."
1) Turrets - This is obvious, if they can shoot you, you can shoot them. And eventually their dice will fail them and you will win.
2) PS10-11 - This is especially useful if you can BR or Boost to change your final position. Not only do you have a much better chance of getting the Phantom in arc, but you're much more likely to do damage against their 2 agility
3) Involuntary stress - A single stress token will require the Phantom to do a 2 bank, 2 or 3 straight. This eliminates their favorite move (decloak left, 1 turn right) and prevents them from turning in ways that you cannot. This works even better if you can do it before they shoot, because then they can't cloak.
4) Ion - If you manage to get an ion hit through (27% 3Fv4F, 60% 3Fv4) then it cannot decloak. Furthermore, it's going 1 straight and can potentially do a barrel as it's only movement change. This makes it super easy to hone in on, and therefore kill on the next turn.
5) Block decloak - I wouldn't even bother trying this against Echo, but against Whisper, you can typically look at the board position, and rule out one cloak as not useful (typically due to a rock being in the way), a second one will leave her without a shot, meaning there's really only 1 option that's worth blocking. If you do block that path, then you force her into a suboptimal location. For the empire, a basic TIE fighter does a pretty darn good job at blocking this with the built in barrel roll action, a pretty good dial (well, it's the same as the Phantom dial), and a cheap disposable unit. For the rebels, it's a bit more challenging. Z95s are good because they're cheap, but they can't finesse their final position. B + E wings are good because they have a barrel roll, which is the best thing for phantom blocking, but they're much more expensive, though they are also better ships that can bring more to the table.
6) Separate it from its friends. This can actually be accomplished relatively easily throughout the game, starting with the beginning. A phantom more often than not likes to slow roll the beginning - the first turn they want to cloak, so they want to make sure you don't have a shot on it since you'd then have a FREE shot on it. 2 turns are common, and typically towards the middle of the field (since they typically start on the flank). If you bum rush with 4 and 5 straights, preferably with boosts - then while you typically don't get a shot that turn, you're in a great position to FORCE the phantom to either disengage and keep running, or to alter the plan and turn in to give support to the rest of her squad, at the expense of getting shots on the phantom. Either one is a win for the opponent. As the game progresses, if you do large sweeping turns away and then come back for another attack instead of just K turning and jousting, you will separate the Phantom from the rest of the squad more often than not. The Phantom will typically chase where as the rest will be K turning. This creates separation where you can attack the Phantom alone.
7) Get behind it. Easier said than done, but if you attack it from multiple fronts, she will turn her back to someone. From there, you can slow roll with the one that is behind, while bugging out with the others. If done properly, she won't have a shot. Which forces either a cloak action, or staying uncloaked. Either way, you have a better chance of getting damage through a tokenless 4 agility target, or a 2 agi target with an Evade.
8) Bombs. Well, specifically mines. This goes along with blocking decloaks, but Proximity mines can and WILL wreck Phantoms. Keep in mind that they will move after you, and with the new changes to Prox mines, your bomber or Firespray can just drop one ontop of the Phantom, or in its decloak path. Proton Bombs and Seismic charges are a bit more difficult to manipulate to actually catch a phantom in arc, but with proper placement, it can be done. But I would suggest using mines over either of the others. And for those of you complaining that the mine can whiff and be 3 points wasted, the chance missing completely is 87.5%. The chance of landing at least 1 hit 3Fv4 is 40%... You are TWICE as likely to whiff on your attack than with the mine.
9) Ordnance. One of the problems with Phantoms is getting through 5 dice at R3 is next to impossible, but getting them in arc at R2 or R1 is next to impossible. Solution? Ordnance. A Concussion missile shot with a focus yields 3.68 <BOOM> at R3. The Phantom will be rolling 1.5 <Evade> if it doesn't have a focus, or 2.5 <Evade> if it does. Either way, you're getting damage through.
10) Action Stacking - I alluded to this above, but if you can stack your TL+F, then you'll make each shot count just that much more. This can be accomplished via Squad Leader, Airen (who coincidentally was released at the same time as the Phantom!), Kyle, PTL, Garven, Field Officer, etc. Heck - a Green Squadron Pilot can act as a Squad Leader to a Rookie and two Blues w/ HLCs. Or you can shave a few points off, and put EI on the Green (who will easily be doing greens to stay in formation) and not even lose your own action.
11) Roll lots of dice. You can do this multiple ways - HLCs get you 4 at a time, or a 7 TIE swarm gets you 7 sets of attacks. Sure, the law of averages says that you really shouldn't do that much damage, but those green dice will fail, sooner rather than later.
12) Combine the above! Few of these alone will always beat a good Phantom, but you can combine them in ways you might not have thought of before to get a kill. For example - how many of you have taken Corran w/ VI, FCS, and APT before? This combo allows him to move after Whisper, which allows him to setup a R1 shot, where he takes the Focus action. And he's more than likely already taken a shot, which means he already has a TL. Now he unleashes those APTs, and it's a dead Whisper. Oh, and it works against Fat Ships too!
Or how about 3 Scimitars with Proximity mines? That leaves you with 43 points - plenty for Fel and two IPMs. Now you've combined #2 with #4 and #8. Heck, you could even swap one IPM out for two Flechettes to add #3 to the mix!
Full squads do not have to be designed to take care of Phantoms, but it's very useful to spend the last few points as upgrades to address it. I honestly have had pretty good luck thus far with Ordnance, and I'm super excited to try my Gold Squadron Pilot out with a Proximity mine and an Ion Cannon Turret. Through in R3-A2 for good measure, and you have a 28pt control BEAST.
What else have you found to be effective against Phantoms?