I've had the MDR-1000x and QC35 together for a little over a week now. I've owned the QC35 for a couple of months now and I picked up the Sonys a little over a week ago. I should also note that I have the New Bose QC30, as well as the Bose QC20i which I've had for a little over a year now. I will give you my ranking between the QC35 and MDR-1000x based on Sound, Comfort, Noise Cancelling, Features, and Design.
Sound:
This is really not close for me. The Sonys are Clearer, More Detailed, Tighter, More Musical, and Plays louder on my Ipad Pro and Iphone 6S Plus. It's honestly the best sounding Bluetooth headphone I've heard, just beating out my previous favorites, the Sennheiser Momentum 2.0 and V-Moda Crossfade Wireless. The only area where the Bose wins for me is in the Sound Stage. The QC35 does have a deeper and wider sound stage. Instruments for Acoustic music have more space around them. This can be good for some music, but causes more energetic music to sound kind of boring. I also like the Dynamic EQ on the QC35 that adjusts the EQ based on the volume. I find it useful in certain situations. Mainly when I'm in bed next to my wife at night watching or listening to something exciting on my iPad and I need to keep the volume lower. Keeps a level of excitement at the low volume.
(Winner - Sony)
Comfort:
The results here are different for me than many. I have small ears and I can wear both of these headphones for hours with no discomfort. The Sonys have a snug fit. Feels more secure on my head. The pads work better with my glasses than on the Bose. However, the Bose have wider openings in the ear cups that completely surround my ears. The padding on the headband of the Bose feels ever so slightly more comfortable. The thing with these headphones for me is I prefer the comfort of one over the other in different scenarios. If I'm sitting down at a desk, or on the couch, not doing much moving, Bose wins. You do forget you're wearing them. If I'm moving around, doing work around the house, or walking the dog, I prefer the Sony's as they fit more secure on my head. The Bose moves around a little more on my head than the Sony's. I was really considering declaring this category a draw, but after further consideration, I'm going to give the slight edge to Bose on this. I do most of my listening with these headphones sitting down as I tend to use my QC30 when I'm more active. It's really close though.
(Winner - Bose)
Noise Cancelling:
I wear glasses and have tested both with glasses and without. With glasses, after running Sony's Optimizer (An amazing feature by the way), they clearly best the Bose. It really is amazing how well this feature works. I honestly thought it would be a gimmick. I can't explain how they do it, but this is the first pair of noise cancelling headphones I've ever used where I didn't feel like I needed to take my glasses off to get that little bit of extra silence out of the headphones. Remarkable! Bose has always struggled with my glasses for me, which is the reason I even got into their noise cancelling earbuds to begin with. Now when I remove my glasses, which is how I assume most wear noise cancellers, it's very close. However, one thing gives the Sony's the edge for me, high frequency noise cancellation. The Sony's cancel the sound of silverware banging together, running water, voices, and other sudden higher pitch sounds better than the Bose do. They both bring the bass from my home theatre system to a near whisper, and I'm hard pressed to tell a difference. I will say that I've only tried the Bose in the Air so I can't compare the two for airline use. With these facts, I'm currently giving the edge to the Sony's assuming they're comparable to the Bose in the Air; which every review I've read state that they are.
(Winner - with Glasses, Sony by a Landslide. Without Glasses, Sony by an inch)
Features:
Sony has the Noise Cancelling Optimizer, Touch Controls, and Awareness Modes. You can use the Sony's with Noise Cancelling on or off in both Bluetooth and Wired Mode. Bose has Voice Prompts and Dynamic Multi Device Switching. Most say the Sony's, I say it depends. The dynamic multi device switching that the Bose offers is a very big deal, and in my opinion the best feature out of all the devices. I mean, being able to connect to my iPad Pro and iPhone at the same time and have sound played from each one without going into settings or repairing through the headphones is a huge deal. For me, I'm going to give the slight edge to the Sony's for 2 reasons, first, the Noise Cancelling Optimizer is a God send for me and my glasses. I finally can wear Noise Cancelling Headpohones and never feel a need to remove my glasses. Second, I own the QC30s which offer the same Multi Device Dynamic Switching the QC35s do. So the feature is available for me.
(Winner - For Me, Sony. For Those without glasses and/or those who own the New QC30s, it Depends.)
Design:
I've never been big on design or build quality. Both look decent as Consumer style headphones, and both feel premium, although in different ways.
(Winner - Draw)
Final Verdict:
For me it's hands down the Sony MDR-1000x. It has better sound and noise cancelling with my glasses. Sound and Noise Cancelling are what matters for me most with these two headphones, and the Sony's win in both. Owning the Bose QC30s actually make it even easier to choose the Sonys for me. If I didn't own the QC30s, I could see it maybe being a little tougher to decide simply because of some of the features the Bose offer that the Sony's don't, as well as the amazing comfort. Your mileage may vary, and I encourage each person to try out both if trying to make a decision.