Please do correct me if I'm wrong.
Graphical Enhancements:
Bump Mapping
Fresnel Ramps
Reflection Mapping
Specular Mapping
Self-shadowing
Various effects (Sun Glare, Light Bloom, Sun Glint)
Water Relflections
Ground Reflections (During Rain)
Building Reflections
500 Autogen in 1 scene increased to 5000 Autogen in 1 scene
New Features:
Camera catch-up (During pitch, bank, yaw, acceleration, decceleration)
View categories, with multiple new views (e.g. tail, left wing, landing gear, etc.)
Missions ( tutorials, challenges, adventures, etc.)
Supports 5.1 Channel Sound
Can output environment noise through speakers, navigation and ATC through headphones
New multiplayer system
Ability to play as Air Traffic Controller in multiplayer mode
99,999 feet barrier has been raised by a significant amount
Over 10,000 accurately placed stars
All lunar and solar cycles are set up according to real life
New Traffic:
Cars, Boats, Trains, Animals (following actuall migration patterns)
Enhanced Airport Environment:
Airport Vehicles (baggage carts, service trucks, etc.)
Moving Jetways
Weather system completely re-worked
Advanced graphics options to support different styled flyers
Skinning and bones with inverse kinematics (IK)
Improved water physics
Different object types which interact accordingly to location
Moving landable surfaces (e.g. boat helipads, aircraft carriers, etc.)
Gliding:
Auto-generated thermals
Towing system added with rope physics
Entire Software Developement Kit included with Deluxe version. Mission creator/editor included.
I'm sure there is much more stuff, but I can't think of more within 5 minutes so there. Correct me, add stuff, and I will change the above according to the actual things...