Navy could still have its niche carved out, certainly. Water could be used to provide "sneak-around" territory for amphibious units, could be used to provide mobile fire support from the sea.

Besides that, nothing to say the game couldn't add more "non-hovering" units, or bias the third race to be completely non-hovering.

From where Ashes is now, it would take quite a bit of rework to remove hovering from most of the units, just for the sake of adding in navies. The PHC Agamemnon hits the bombardment itch without needing a boat.

Everything hovers, what's the point of naval units?

 

One thing I would like to see that's probably easy:  A better ability to run away.  The units are obsessive about chasing down opponents, often to their detriment (say, by luring air units into a bunch of AA) and I just had a very annoying experience--two regions were close together and I hit them with a fairly large army of frigates.  The regions had never been captured so they were still spawning--and my army turned back and forth, back and forth.  Getting it to actually go capture a region took several tries.

 

Related, there's no good way to make something stay put.  I was against the AI, I put a juggernaut on guarding a repair bay (part of a outpost with a lot of guns).  An enemy dreadnought came along and blew away a good portion of the outpost--huh???  I repaired and watched what happened--the juggernaut was wandering around over a substantial distance (it was wandering into space I controlled), taking it far enough away that it wasn't reacting to an attack on the front edge of the output.  Too bad there's nobody on board to take out and shoot for dereliction of duty.

 

Something else I would like to see that's not on the list:  A point defense defensive emplacement.  It would be a short-range AA gun that would be capable of shooting down incoming bombardment weapons.  A couple could stop an artillery dreadnought's rounds but they could be taken down by massed fire.  Perhaps this would be substrate only as they're the ones with the problem--PHC rounds coming in from behind terrain that means a long way around or an air assault (probably into heavy AA).