Fleet Command and Dangerous Waters are both great games. The major difference is how they're played and what perspective you interface with them.
Fleet Command is a real-time naval strategy game from the perspective of the Admiral. You literally control the fleet or naval battlegroups from 16 different countries. In this role, you direct the major assets strategically and tell your units what to do, when to launch aircraft, where to go, weapons to use, targets to ID, targets to engage, etc.
Dangerous Waters puts you into 1 of 7 different and unique platforms. You can command any of the 688(I), Seawolf, Akula SSN, a few versions of Kilo class SSK, P-3, MH-60, or the Oliver Hazard Perry guided missile frigate. In Fleet Command you don't actually work any of the platforms sensors, other than tell them when to turn them on or off. In DW, you can actually work the sonar stations, the acoustic stations, the radars, TMA, fire the weapons and work all the stations relevant to accomplishing the missions of these naval units. You are simulating being a member of the crew or the platforms captain. You're not giving orders to launch weapons like in Fleet Command, you are firing the weapons.
Both games are very enjoyable. I recommend you get both for what each offers. You will get a different and enjoyable experience from each.
