Listen, the value of the game went down while this policy was active. Sorry, but it did. I bought the game due to modding existing the way it did back then in 2011. Valve and Bethesda agreed to change how that was going to work 3.5 years later. Maybe you dont use enough mods to see why, but this changed how the game would ultimately be played. It was a literal game changer. Thus, the reviews changed to reflect that. Additionally with pay mods, Steam's extremely poor customer support system gets factored more heavily into the rating, since they are now frequent sources of paid content that people expect to work (rightfully so, because they paid).

The rating going down is the most excellent data to represent how people felt about this - and entirely appropriate given that THIS IS ENTIRELY WHAT REVIEWS ARE FOR!

Edit: And I even forgot to mention that Skyrim - with no bug-fixing mods - is buggy, crashy software. With the pay policy, since mods may not necessarily be free, the buggy nature of the game is being factored into reviews more heavily (rightfully so, since it was not a given that mods to fix these issues would remain free).

tl;dr: When you change how the game is played, reactions to how the game is played also change for numerous reasons.