There are some pretty fundamental changes you need to make to start with: game turn time (how long is a turn, and be accurate) - this will dictate distances various things can travel.
Then you need a set ground scale, and one that makes missile movement times realistic - people need the time to react to incoming missiles with their movement (if they can detect them) given that engagements can plausibly happen out to 250NM or even beyond on a typical 'table'.
I think the basic change you'll have to make is a move away from AD for shooting (or really change the amount of 'damage' for each ship, as well as upping the AD for individual missiles), and away from aircraft 'groups' - aircraft will become discrete, but be at higher PLs - most aircraft these days can individually carry sufficient ordnance to cripple a warship outright.
Then you need to consider different altitudes - the only really key ones, I suppose - are very high (where certain aircraft can't operate, but others can) and very low (where sea skimming missiles buzz around, and where helicopters need to be in order to deploy dipping sonars).
Some missiles and guns will be capable against very low, but not very high targets. Some against all... so on and so forth.
For submarines you probably could do with 'deep' and 'shallow' - in the latter case, you need to be shallow in order to deploy most anti-surface weapons, like sub-harpoon or sub launched tomahawks.
For simplicity's sake, you could adjust detection chances depending on the depth the boat is at.
Then you need to apply appropriate sonar ranges to the various different sonars, but consider issues like masking and propeller noise (some sort of 'pie plate template with the appropriate wedge taken out).
For towed arrays, you need to throw in a special action that disallows turns and restricts speeds when deployed, and takes a certain amount of times to throw it out or reel it in.