Here are some ideas I gathered up in 5 minutes
Support for legs, on ultra long haul, instead of two separate flights, allow us to refuel the plane and keep counting it as one long flight, saves time and effort.
Better reward for perfect flights, and I mean, a visible positive number, instead of 0. Something like "Well done pilot, perfect flight. +100 PP points". Also it could be that different flights yield different amounts of points if done perfectly but those "higher paying" flights also yield bigger penalties if done wrong. An example is a special mission in the EHM Business that youre transporting 5 VIPs, where you have to be extra careful with them, or else the company's reputation would suffer.
Extra points if a flight is "successful" after a failure... Like a nice landing on 1 engine.
Extra points if the conditions at landing are very demanding, like strong crosswinds or near zero visibility...
Some sort of graphical user interface to see where the planes are stationed... I mean, there could be a plane stranded in some weird place for months without anyone knowing, this way, by checking a map, someone would go "What the hell is that 767 doing in Congo since september? Let me bring it back to a main hub...."
Could also use this to show where our pilots are stranded

(this would use the same kind of map our ACARS currently use)
Maybe a newsletter that can be posted on the pilot's lounge that will bring the latest news to the pilots... Like... "EHM Informer
Mariano De Ascencao just crashed our last 757 this morning just outside of Rome. Passengers survived but the plane was totaled and this pilot has received a penalty of 5000 points"
... Scratch that last idea

Randomly generated missions, that yield more points than usual. A little script that would just randomly pick a cause, a descritpion, an airplane type and destination for the pilot from a bunch of pre-made sentences... Example
"Mr. pilot...
One of our A320 had a malfunction and had to do an emergency landing in Panama City. The pilot is under investigation for suspected pilot error so we need you to retrieve it and bring it back to the Atlanta hub. Emergency repairs have been done to the plane and it is in flying condition but we would want it back in a EHM hangar as soon as possible. Please reply before (insert date here)
The EHM Management
Accept? [Yes] [No]
Something like that... maybe thats too much to program but it would be interesting to see which scenarios our management would come up with =)
Of course the cause for the mission, the kind of plane, the airport and destination airport are randomly generated and have to be of a class the pilot can fly.
Just my 2 cents...