Ok, this is not a complete rework, but I have some ideas that can really help Nautilus (His passive doesn't need any changes)

Q: Dredge Line/Dredge Spin:

After hitting Q Nautilus will get ready to use his anchor:

Left Click: Nautilus will throw his anchor (With more range) that will stop on the first enemy or terrain hit, if Nautilus hits terrain his cooldown is reduced by 50%

Right Click: If you right click Nautilus will spin his anchor around twice, any enemies hit will be positioned in front of Nautilus, cooldown reduced by 25%

To cancel this ability you must press Q again

W: Titan's Wrath:

When activated, Nautilus will boost all of his stats for a period of time, he can also stack Titan's Wrath into enemy chapions up to three times. Nautilus will also gain five shields that protect him from passives like Darius' bleeding, Talon's Q, Twitch's dealdy venom, and even Titan's Wrath itself. After being hit with one of these one shield will break, if all shields are broken Titan's Wrath will deactivate with a reduced cooldown. 

Note that hitting an enemy with dredge line will stack one stack of Titan's Wrath.

Hitting an enemy with dredge spin will stack two.

E: Riptide:

Riptide doesn't change much, all I want is a faster animation

Also, if an enemy is hit at the edge of the range of Riptide, the enemy will be stunned

R: Depth Charge:

This one is difficult to explain

I think it should work like the R he already has, but he will be able to select up to 5 target enemies with a greater range

After the abilty has been casted, Nautilus will fire something kinda like what he has, but it will split up and speed up depending of the number of targets.

So, there is my idea of how Nautilus could work, that I think it would make him a very strong champion.