So, returned the MDR-1000x and got the PXC 550 in its place. Some early comparisons so far:
Sound
The PXC 550 is more bass-oriented, but also more treble-hot. More V-shaped compared to the Sony. However, soundstage is quite superior on the PXC 550. Both are markedly better than the QC35.
Build
As stated before, my MDR-1000x had creaking problems. Worse, the second pair I returned had some hairline cracks near where the screws go. Never heard anyone else have problems, so I'll dismiss that. The PXC 550 is much lighter, which gives the impression that it's more cheaply built. However, I digress: tolerances are much tighter and despite the plastic, absolutely no creaking or cracking noises at all.
Aesthetics
The MDR-1000x is chunky and fat: the pictures really don't do it justice. The PXC 550, however, is slim and long. Personally, I prefer the PXC 550 by a country mile: the sleek matte exterior is much more palatable to me compared to the faux leather finish. However, I prefer the MDR-1000x's leather pads appearance: they appear much more 'sculpted' compared to the rough finish on the PXC 550.
Comfort
PXC 550 all the way. The MDR-1000x consistently touched my left ear, whereas the PXC 550 is much thicker and thus never had such a problem. Also important to note that the design of the shape is important to consider: the PXC 550 is wider on the top than the bottom, thus accommodating the ear better. That being said, the MDR-1000x is not what I'd consider 'uncomfortable', just that the PXC 550 is even more so. Also helped by the fact that the PXC 550 is incredibly light and has substantial headband padding.
I find that the MDR-1000x seems to be designed with bigger heads in mind, as I only had to use 2 clicks on either side for best fit. The PXC 550, on the other hand, required me to go beyond the half-way point.
Controls
The MDR-1000x has flawless gesture recognition. Really, it's insanely accurate, and it's never misinterpreted my gestures. The PXC 550, less so, but still very accurate. However, the PXC 550 has a lot more gestures, so much so there's a 48 page manual available for it. I especially like how a double tap instantly turns on the external mic and stops your music, far superior to holding your right hand over the cup for the MDR-1000x. Both are excellent.
NC ability
Ultimately, the MDR-1000x is superior when no music is playing. Once music is playing, that advantage disappears, and both do a very good job. In addition to the NC, the MDR-1000x also has 'ambient' modes, which turns on the microphones and allows either all frequencies or frequencies centred around voices to be passed through. Very useful.
However, the PXC 550 has an adjustable level of NC, which is great for those who feel less need for NC and more relief from the 'pressure' effect. Both cups have it, though the PXC 550 has quite a bit less of it. The PXC 550 also has an ambient mode (TalkThrough) which picks up everything.
Accessories
The MDR-1000x has the superior carrying case, being a rigid box. However, it was also bulky and couldn't really store anything besides the flight adapter in it as it has no internal pockets. The outside pockets are, frankly, a joke: they could barely contain the headphone cable, let alone the charging cable. The PXC 550 is semi-rigid, but has internal carrying pockets to carry everything.
Both have a headphone cable, flight adapter and a charging cable. The PXC 550's headphone cable is a 2.5mm jack, which while not as common as a 3.5mm jack, is still quite common. However, it also comes with a 1/4" adapter. Also important to note is that the MDR-1000x's cable does not have mic controls, so it's essentially a dumb headphone when you connect the cable in. Personally, I prefer the aesthetics and feel of the MDR-1000x cable, being very anti-prone to knotting, however I'd prefer a mic cable.
USB cable is a USB cable: both are type B. The PXC 550's one is longer, as it allows you to listen while charging. The MDR-1000x turns itself off when you're charging it.
App
The MDR-1000x has no app for it. The PXC 550, however, has an app which has a gimmicky UI but allows you to customise features of the headphones which are unique to it. Inside it, you can adjust the Smart Pause feature (which is amazing IMO) as well as the various DSP modes (honestly, pretty pointless unless you're listening to podcasts or audiobooks).
Conclusion
As much as I loved the MDR-1000x's NC ability, hefty build and excellent carrying case, ultimately the creaking was the deal-breaker as well as its weight. Funnily enough, the PXC 550 costed me more in the end of the day due to the substantial discount I got for the MDR-1000x. Provided that the creaking is just an unlucky occurrence, both headphones more than punch their weight and provide excellent sound with excellent NC. Both will be excellent (albeit expensive!) purchases.