Anyone who is using Phantom in neutral is using it wrong imo. Phantom is primarily used best to force them to do *something* you can punish.
Smart players will see you charge and shield or jump over it, yes.
You use it during advantage. For example, someone runs in on you with a dash attack and you shield it. You downsmash to punish, and instead of chasing them, you charge the Phantom. You can use it to tech chase, punish them trying to punish you after they get up, or if they roll back you have a free Din's fire.
Phantom allows Zelda to control space, and you cannot control space in a smart fashion if you're not already at an advantage. So, what I've been doing at low percents is:
Fsmash > Charge Phantom
Jab > down smash > charge phantom
Grab > Down throw > b turn charge phantom > overhead slash.
The overhead Slash is truly the best one, because the hitbox covers a lot of punish attempts. Its extremely fast too for what it does. If you charge too much, Phantom level 5 will whiff, or you'll be hit while your Phantom is on standby.
I also believe a lot of you aren't using the fully charged phantom to your advantage. Something I've been finding a lot of success with is charging a standby phantom and immediately running away or towards them, then immediately detonating it. What this does is it makes your "approach or run away safe.
So in theory:
Charge Phantom fully > dash > detonate phantom > roll cancel dash grab
What this can do is punish an early jumper trying to dodge it.
Also, you want lots of bturn phantoms. Jump away, b turn phantom, and you're charging and moving away as they're coming at you, giving you enough space to punish them.
Or, you can start tricking people by charging the phantom the opposite way out of a dash, or for edgeguarding. I've punish several Ike's for recovering onto stage with their side b by running to ledge and charging the phantom the opposite way and then pressuring them.
Nayrus love is seriously a get out of jail for free card, up B out of shield is still god like.
One more thing I've used is charging a phantom and then teleporting in place. They'll jump over the phantom and if they do, and try to punish you, you're punishing them with a kill move.
Zelda is incredibly tricky and still requires a high skill level. She is definitely a high tier character. There's going to be a huge skill gap between good Zelda and bad Zelda's now, due to the mechanics and flow/pace. Zelda still has to be played super safe. We're not inkling, we can't just throw out attacks and get out of Dodge for free. Our moves are powerful but risky. Keep space from your opponent. Don't just go nuts on approaching and attacking. Shield grab, Nayrus.