Atom's powers are limited only by the skill and imagination of Chronos (and Zeus...) scientists. As long as they keep creating tougher hides, stronger bio-blasters, fitter physiologies and more spectacular superpowers, and forgetting to protect them with an anti-Aptom antibody, he's going to get periodic boosts as and when Takaya-san considers it necessary to the plot and comes up with another awesome design.
Known Zoanoid powers we have not yet seen him use include sonic attacks and complete immunity to HF swords. Even Guyvers don't have that last one; if Guyot gets a G-unit, and Aptom eats an Enhanced Zerbubuth (we have seen some reproduced HZs and Z is one of them), he would be able to engage at close quarters and just trade HF blows (and we know he has better HF reach than a Guyver).
I don't recall him using a barrier, but we've seen a HZ with one (that had a much bigger range, proportionate to body dimensions, than Gigantic), so it's only a matter of time until he incorporates one of those into his tendency to absorb a highly specialised Zoanoid and incorporate a far stronger version of its speciality into his general purpose form.
The Libertus can punch holes through the 'regular' Hyper-Zoanoids from which his powers are derived, and a mere pair of Unus can eat a Libertus alive. (If Aptom made some clones with Unus bodies, could he create a gestalt with himself?) Whether or not there's any left of either, he has certainly not yet absorbed the strongest meal there is.
I don't see why gravity attacks necessarily require a zoacrystal - at the very least, Barcas might well figure out how to install gravity orbs on a HZ, which would also enable levitation. And, Aptom just needs to learn how to make one orb to give himself a battery.
Dyme was an extraordinary case, but Somlum's molecular glue could probably be replicated, given enough time and resources. It'd be pretty much a win-button against a nude foe that can't just shed and regrow affected dermis and limbs.
His cloaking ability is likely an EM manipulation trick, which opens the door to Chronos developing the gamut of Magneto's repel-a-planetary-invasion capabilities. And Aptom cranking them up to eleven.
Uranus bio-engineering is known to be able to bestow the abilities to teleport and to fight in a hard vacuum. We've yet to see a Zoanoid do those, but I'm pretty confident he's already got full aquatic adaptations on file.