My family owns both. I use the WS-99's as my commute headphones and bought the M50x's for my wife to use with her portable players.
The M50x has great sound and is slightly more comfortable than the 99's; however, the sound profile on the 99's is far better than the 50x's. I have had the 99's for a year, so, I broke the m50x's in with 200 hours of music before comparing them. The sound stage is slightly wider on the 99's, the midrange is more forward and the bass is deeper, tighter, and more visceral (guess that bass chamber does make a difference). When I hooked up my JDS Soundlabs portable amp, the difference become even more pronounced; it's probably because the amp lets those bigger drivers in the 99's out to play.
To be honest, I did not expect the 99's to be better than the M50X. I was a bit worried that I had bought a weird, dead-end headphone from AT because I hardly ever hear it mentioned here. I was pleasantly surprised at how well the 99's did against the M50X's. I also like that I have a set of phones that doesn't look like every other cookie-cutter phone out there. I get plenty of questions from Beats owners and enjoy letting them try them. I don't talk down the beats, I just let the AT sound speak for itself.
I know that some have mentioned pain with the 99's. I have a massive noggin and normal sized ears. I minimized the possibility of pain by stretching the band. To be truthful, I haven't had any pain. I will say that the oblong cups on the M50x are slightly more comfortable, but I wear my 99's more than 2-hours a day and have had no issues.
I noticed that careful shoppers can get the 99's for around $179 now, vice $169 for the M50X. Hope that helps.