Mutt,
I don't like the fact that things like 30-45m runways are tied to the aircraft performance model tables that the program uses rather than the airfield data file.
This means that if you have an airport that has 30 and 45 m runways such as Brisbane (and others) you have to use a different aircraft configuration for each runway - ie you can't select 14/32 and have it automatically use the narrow runway data, and then select 01/19 and have it use the 45m data.
From a management perspective it means that you have to have double the aircraft tables (normal and narrow runway) - which is a pain, but it also means that you have to break up your airfield data so that people don't have access to the narrow runways when using the normal runway data.
From a user perspective the same dramas apply - you have to leave and re-start the program to switch between narrow and normal runways - confusing for those of us less comfortable with computers.
There are a couple of other issues with it as well, but I can't off the top of my head think of them - its been a few months since I used it.
It has its good points, don't get me wrong, but with some operational input at the beginning (and I don't mean the guys that fly at Boeing - but real airline users) it could have been significantly better.