Thats the question on most wannabes minds. Its been done here on pprune so many times, and yet there is not always a clear cut answer. I'm trying to figure it out myself at the moment as I hope to start training this coming summer
One point is that airlines in the past have been getting CV's from CAP509ers and 'Self-Improvers'. With the JAA system, the self improver method has been replaced with he Modular system, and airlines may not have that much experience of these students yet.
I guess the Modular system has been designed to either reduce the employability differences between new 509/Self Improver FATPL holders OR to reduce the course and cost difference, hoping most people will choose to do an Integrated course
I'm leaning strongly towards Modular on an integrated timescale. Hopefully, like with most qualifications getting that job should be based on your results e.g. first time IR pass, good marks in written ATPLS's.
Just my take on things.
Good luck, JT8