Most of these settings are completely personal preference, bearing in mind performance. I use the same as @Art_P for Time before departure and time between cruise traffic.
Substitutions - I personally prefer no substitutions as I'd rather lose a few schedules for the sake of not seeing blank liveried aircraft that you see under fallback textures.
Wingspan - I would recommend having the wingspan options set to either compatibility mode Low or High so that aircraft will spawn at poorly optimised default airports. The High settings allows more widebodies to spawn at these airports however it increases the risk of overlapping aircraft when parked.
LOD setting - This is dependant on your hardware. On my machine I have no issue setting this to High, however if your FPS suffers you may want to say at default or even low. It will reduce the visual quality of aircraft at certain distances though.
Texture Detail - If your graphics card lacks VRAM and you are getting stutters then I'd recommend setting this to low. The textures on the aircraft will be slightly lower resolution but unless you very close up to the aircraft, its barely noticeable.
Database selection - Totally personal preference. I personally prefer the winter schedules as there are a few more flights at my favourite airports.
Hope this helps
John - Just Flight.