The .sit file is the closest thing we have to a "normal" save option. It saves as much information about the flight model as possible in order to restart in the same set up.
There are some known bugs with .sit files--the 737 Xlua scripts prevent the gear/flap from loading in some cases, for example. We also do not save some info in .sit files on purpose as it bloats the file size.
If you have found specific things the .sit doesn't save properly with default aircraft (we make absolutely no guarantees about how third party acf handle .sit files), please file a bug here with a copy of the .sit file, and the exact steps required to see the problem.