Phantom Ganon is not a particularly difficult boss, however his attacks do deal a large amount of damage. Elixir soup is especially helpful during this battle. While Phantom Ganon is charging up a lightning ball to throw at you run beneath him and use a quick spin to bat his attack back at him. Being beneath him, he will not be able to knock it back at you. Use jumpslashes and quick-spins to then finish him off.
If you are visiting FF2 early to obtain the Master Sword early, it is important to note that it is impossible to deal damage to Phantom Ganon without the Master Sword. Due to this oddity, you will have to skip the fight.
There are multiple wind waker dive spots both inside and outside of Forsaken Fortress that can be used to get around Phantom Ganon (images to come). After successfully diving, swim to the only loading zone accessible from the water (the one behind the big wooden door).
Note: Depending on what dive spot you are using, you will have to be careful to avoid the Phantom Ganon cutscene trigger! However if you do hit the trigger by mistake, you can simply use the dive spot pictured above (visual soon to come).
Once you've gotten inside and bypassed Phantom Ganon, head to the right a few rooms until you get outside by the search light. From here, you can either attempt a hover directly to the loading zone of the Helmaroc battle (using the telescope to align with the big doors will help), or hover up near the doors, heal with Tingle, and then do another hover and use a red Ting and the deku leaf to reach the loading zone. Multiple methods to skip Helmaroc King can be found here.
When sailing towards Forsaken Fortress, stop at Child Isle and perform Dry Storage. Sail northeast of Forsaken Fortress until you see an outpost. Get Chest Storage on that outpost and sail to Forsaken Fortress. Walk up the walls and you will walk through them and fall into the water, similar to the above method. Get back on ground and walk past the Phantom Ganon loading zone. Now simply walk up the walls as shown in the video below and enter the loading zone.
Humorously enough, you can skip the majority of the Phantom Ganon battle in Ganon's Tower by simply knowing what doors to go through to get to the light arrow. Here is the proper order of doors in order to get to the light arrow: back, left, straight, left, right, straight. After obtaining the light arrow, simply shoot Phantom Ganon with one to defeat him.
Although it is possible to skip the Phantom Ganon battle completely (methods to do so can be found here), doing so is often avoided because of the extremely lengthy and difficult hover necessary to skip Puppet Ganon--as you do not have the light arrows to defeat him. Due to this reason, the entire fight is not usually skipped, except for in segmented runs and TASes.