However, now we are developing real time fixedwing firmware and you are right, the burden of history is present. The best way to fix this would be refactoring the fixedwing code (e.g. autopilot structure, control loops etc.) to follow similar style as rotorcraft.
Benefits are way clearer code, possibly performance improvements and also easier change of the control loops/navigation routines (imagine you want to use your own control loop). Unfortunately it is a lot of work and lot of the code will have to be marked as obsolete.