There are a ton of factors that play into refueling and defueling an aircraft. No two jets are alike, just like no two fuel trucks, or fuel pits are alike. Some jets, due to age and other factors can be slower at refueling. As far defueling goes there's also factors there, for example. If you bring a navy jet back to the ship, and it just refuelled from an airforce tanker, you can forget about defueling it, or even putting it in the hanger. JP-8 is more volatile than JP-5, therefore you'll have to spin the engines up, and burn the fuel out, if it's scheduled to go to the hanger. You can't pump jp-8 back into the ship's fuel supply, due to possibly making the entire stock more explosive. After you burn the fuel out you refuel it, to further dilute the JP-8, and the flash point is tested again. If it's still too volatile you repeat the process. That can take hours if you need to burn off a few thousand pounds, especially if flight ops are going on and the deck boss won't let you go above idle because of it, you're talking 420-700 pounds-per-hour (per engine) at idle, vs. about 2000 pounds per hour at 80% N2 which was the highest we cold run the engines without rigging it for a high power turn.
Being deployed away from your main base also causes issues when it comes to even basic maintenance. Sometimes parts are scarce, so even a simple maintenance task can take hours, if not days due to a lack of spare parts. Sometimes the only option is to rob a jet that's hard down to keep the rest of the jets flying. When major issues, like combat damage, come into play your only option may be to just hanger the jet and rob what parts you can. In real life you may have to fly in tech reps from the company that built the jet (being that you may now have structural issues to go along with your electrical and mechanical ones) to determine if it's repairable on station. If not the thing may get packed up and shipped home on a transport.
When I was in the navy we had a jet that was damaged beyond our repair capabilities on the ship. We stuck it in a corner, used it for parts, and craned it off when we got back home so it could go to the maintenance depot. While this is probably the most realistic simulator out there, there's things that just aren't going to be modeled because it won't bring anything to the experience.