The thing I have found to be v. frustrating about Fly! is the controls. It's incredibly difficult to configure the controls the way you want them- the process iteself is simple, but the way the thing is presented is bad, very bad.
I also think the flight planner feature is a bit badly designed. too much emphasis on graphics rather than ease of use.
Converting from FS98 to fly! is difficult, but I should reckon that the results are worth it if you have a decent control input system.