Plan types to include approach/departure fixes, unavailable approaches/departures replaced with computed waypoints.
Automatically read AIRAC files - Plan types to include AIRAC approaches & departures options, unavailable approaches/departures replaced with computed waypoints.
Output FSX & FS9.PLN, .rte, and .rt2 files to external directories - proper setup functionality includes security setting of export directories. Export directories settable per aircraft.
Collate external information with the flight generation, approach plates, charts...
More AI control - choosing aircraft, plans...
More Mission types - search and report, search and rescue, follow me aircraft, mystery tours...
Enchained destinations list: Generated flights progress through a list of airports along a route, and return to the start when the list is exhausted
Committed profile setup: set options such as; choose to accept the result, choose save/restore/advance functions availability...
Multiple Parameters setups per plane - hight alt, low alt, fast, slow...
In-Flight Weather menu - weather types, wind speeds...
fsx.cfg, dll.xml, exe.xml, per aircraft - requires FSX closed to restart.

more ideas added below:
P3D full support.
Taxiway names shown in maps.
World maps representing the time of year set in the profile, other functions.
Some new functonality kept a secret for the time being

Airport Subset Generation
Real World Weather support
Mutiple User Aircraft Directories
Random time of day for next flight
Specify the seat count in aircraft params, and per person average weight and max weight per cell
Manually enter fuel amounts