Now, ASSUMING that Time/Season was NOT a factor, I believe I can make a good sum of the changes:
Improvements:
>Sky looks a lot bluer, more natural
>Looks a lot less tropical and more like France
>Lines are a lot less jagged
>Improvements on certain shaders
>The grass no longer looks like Astroturf
>The Trees have seen a lot of improvement
>The bridge at least looks structurally sound now
>Water reflections are a lot more refined
Losses:
>The clouds look a lot less brilliant and impressive
>The overall look is more dull, not as bright and "poppy"
>The bridge lost a lot of aesthetic design
>The shading on the Statue went pants-on-head retarded
However, ALL OF THAT analysis is WRONG because the TIME OF DAY (and possibly the season) is different. In the January pic, one can see that the shadows point towards the "camera" with GREAT length while in the September one the shadows are relatively short. THEREFORE, the January picture was taken a lot later in the day. Since the sun is closer to the camera's field of vision, the sky looks brighter and has less deep of a blue hue. Because the sun is further behind the Golurk statue, the shadows in the January picture are a lot more noticable.
In addition to this, concerns about the literal quality of the September image only compound the problem.
IN SUM, we simply CANNOT KNOW at this stage why either of these pictures looks this way since we do not know the entirety of the circumstances of each. HOWEVER, I DARE you to point me to ONE game that got CONCLUSIVELY shittier in terms of graphics of all things as it went through its dev cycle.
I do not think Game Freak would make such elementary mistakes.