I've played through several BE games now and I have yet to reach a point in which the game was not already decided (more-or-less) by the time I got hover tanks. They are SO late game that claiming they eliminate naval units is pointless. Also, they move slower, the hover artillery (as already pointed out) can't keep up, they receive 25% combat penalties on water and are super vulnerable to krakens. Additionally, I have yet to do an amphibious invasion with them without aircraft carrier and dreadnought escorts. Also hover units are not a match for a dreadnought fleet (which can be upgraded to 3 range, can way outpace hover units, and have devastating ranged firepower).
Naval units are, along with Civ 5, the most important they have ever been in a Civ game. You can't reasonably expect to win a war without them. Aside from moving fast and not having to set up, it's easy to interchange them when they get damaged during sieges, they protect (pre-patch) extremely valuable trade ships from your enemies and they keep those pesky sea dragons and krakens away from your water improvements. every single war should be fought with a large navy.
Do I think they should eliminate one-shotting? Yes, even if ships remain vulnerable.
The AI should be programmed to build significantly more ships
The defense perimeter quest that makes trade units invulnerable to aliens should be removed (at least for sea units)
The AI should aggressively attack trade routes and resource improvements during war, especially naval ones
Aliens should be much more aggressive late game towards players who attack them, attack in force (especially at sea with krakens- I had a group of 5 once spawn and ravage a couple intercontinental trade routes, sent my warships, they didn't even fight back! This was Apollo difficulty), and viciously attack trade/improvements. If you fight aliens, remove miasma, etc. you should be forced to deal with them.
AI should move ships in fleets, stock aircraft carriers with aircraft, aggressively engage smaller and/or technologically inferior fleets, and retreat from larger/more advanced fleets to preserve resources. Cities should be defended from the sea as well as land. I'm so tired of fighting 1 or 2 ships at a time in civ games with fleets of 6 or more ships. Civ4 at least had naval stacks of Doom (though they were rarely a factor- it had to be so late game for an AI to build those the game should already be decided).