Phantom needs way too much work out of any merc to be honest.
His loadouts need a desperate rework. I could probably write maybe a 500 word analysis just about his loadouts as they are and what they should be in my opinion, but I doubt anyone would really be interested so I’m going to skip that.
He doesn’t fill his role either way, other recon mercs can at least get information on enemy location with their spotting abilities, Phantom doesn’t have that and he’s not an assassin either. He just carries a fancy katana and has a stealth ability.
Assassins in most cases have higher damage at the expense of their defenses. Phantom has only higher damage at melee range and compared to kukri or cricket bat there’s only a 5 damage difference.
For and assassin being at 110HP isn’t exactly good either, considering all assault mercs and 3/4 fire support mercs have higher hp than him as well as Redeye from recon. Sure he does have his shield, but currently the shield only has 75? hp(correct me if I’m wrong) and as soon as it wears of you’re at your 110hp. Now assuming you are being shot by the enemy and can’t run into cover, you make the best of your shield and sink as many bullets as you can, but as soon as you return fire you will most likely be at a disadvantage as enemy has their bullets already fired, in the air, while you’re just pulling the trigger. In general I would just like if Phantom had a little more health.
I’m not saying he should be like a rambo assassin, but honestly I wouldn’t mind it, as if he’s too great at stealth he would also be just as problematic. I really hope SD doesn’t make Phantom more melee focused than he already is, at least as he is for the newer players.
If people are afraid that with better stealth he becomes too powerful I wouldn’t mind if he couldn’t attack from stealth and had to go through the deactivating animation for it as it’s not long anyway. Currently refractive armor’s purpose in my opinion should be to enable his flanking power, but it really doesn’t help that much.
The current stealth on refractive armor is rather ridiculous in my opinion, as long as I’m aware of him, he can even be crouching completely still in a dark corner and he’s still no problem to spot. I’d like Phantom’s walking stealth to become what’s his current standing still stealth is and make him completely invisible while standing still if he has to deactivate stealth to attack anyway.
The noise from refractive armor, I would like for it to be gone completely or at least give him more Sneaky augments and buff it to like reduce noise by 75% + or so. I still don’t think it would be overpowered, at least you would feel rewarded from flanking without being given away by your own ability.
The current shield health the refractive armor has. I do think he needs it, as he wouldn’t really have much of an effect attacking from a flank with half his health or so after taking a few shots while flanking. I honestly like the armor part more than stealth about refractive armor. I would like the shield health to be back on 150hp as long as he needs to deactivate it to attack and I doubt it would be too strong on him.
I’m sure many of you have many different ideas for Phantom, but to be honest strong stealth and melee are unhealthy for a first-person-shooter. I don’t consider my ideas nowhere near ideal, but without knowing what SD’s intentions are for Phantom’s role or what type of second ability he might be getting I can’t really come up with much better suggestions from the top of my head right now. I don’t claim to be a Phantom expert or even a great Phantom player either as he’s fallen out of my favorite mercs to play for quite a long time now, but I hope he will get back there sooner than I expect. 
He’s still going to stay my favorite merc as he was the first one I bought and I have plenty of other ideas for him, but it’s hard to balance if I’m not sure what to focus on.
All of the suggestions above are all considered that Phantom cannot attack from refractive armor and has to deactivate it first.