The reason his face looks different is because his subcutaneous fat pads have increased. His face is softer and paler because of a lack of androgens - it's that simple really. JDS lost all of his aggression post USADA, on top of that he got flatlined twice.
Let's not forget that JDS ate countless bombs from Stipe in their first encounter, and never looked rocked once. Then Stipe wrecks him with a single straight punch in the rematch.
His lean mass:fat ratio has decreased significantly. You only have to look at him for a couple of seconds to notice it. Go on youtube and watch an interview prior to UFC 160, then look at one of his post-USADA ones. His face was much more taut and stripped of fat pre-USADA. His neck was thicker/more muscular where his gonial angle met the neck.
He doesn't possess the same shock-absorbing muscles that he used to have in his temporalis, masseter and trapezius/neck region. He's simply less sturdy.
He is not smaller per se, but a lot of the muscle was replaced by fat. A smaller looking muscle can be stronger than a muscle region that looks bigger - the variable is the fat/intramuscular fat content of the muscle. Muscle quality and insulin sensitivity are key here.
An easy way to observe the changes is also to go on gettyimages and search for "Junior Dos Santos portrait" - then you'll be able to find pictures of him over the years in the same angles and poses - if you have photoshop, you can easily layer a couple of pictures from different years and then change the opacity of one layer slowly to reveal the changes. You can do the same by screencapping him over different weigh ins over the years.
Even his hairline changed(yes, I'm aware he shaved it tight - but there's a reason for that). His medial hairline used to be frontally bossing down toward his eyebrows because of the effect of a strong occipital muscle. His center hairline is now set more "up" because of the lack of occipital muscle pulling. His hair will also have lost some darkness/piercing saturation that is correlated with low subcutaneous fatty deposits. He'd look grotesque with diffuse dead looking hair if he grew out his horseshoe now.
A lack of testosterone and DHT simply makes men less virile looking. It's pretty basic science. He's a shell of his former self.
The truth is, JDS got into the sport because he was "fat and out of shape". He's not naturally "lean & mean" - at least not at the 240~ lbs he fights at.