Interesting project. 20 reads and no responses yet. I'll take a crack, Mikkel.
It looks to me like you should use two Arduinos.
One interacts with a panel of user's button switches and sends serial messages to the ROV's Arduino.
(perhaps recycle a game controller for the switches)
The second Arduino is on the ROV. It waits for a message, interprets it and controls the L298N boards appropriately.
I'd definitely use some of the stepper libraries. There are many L298N Arduino shields and programs to see as examples.
This way you can divide the project into 3: Sender-Arduino, ROV-Arduino, and SerialMessageLanguage definition.
Good luck!