I believe the problem here is too many people misuse the word "quality" when they are trying to talk about their own personal preference, which is not covered under the term "quality". Your first paragraph is spot on, but your second is more like personal taste and perspective than quality.
Example one of my favorite games is Chrono Cross. I love the story and themes used in the game, and understand what the game is trying to convey perfectly. However that does not change the fact that the pacing is objectively bad, despite my personal taste. Certain key parts of the plot are missable, leaving plot holes if you don't follow a specific path or talk to a specific optional NPC. There are giant info dumps at the end of the game that tie everything together, then rip itself apart, and put it back together again with yet another info dump BY OPTIONAL CONVOS right before the final boss. It is a very good plot with a lot to offer, but the delivery of said plot lacks objective quality.
The same applies the other way around as well. Just because I do not like the narrative or what the game is trying to convey, that does not mean it is not objectively well written.
So in summation, quality =/= personal preference in any sense. People just incorrectly use the word "quality" as a blanket term when it is not meant to be used that way. At least that is how I have always seen it.
Your whole essay about CC plot and pacing is highly debatable. I don't find the passing bad, I only find the story confusing (and it's very confusing, I've only fully understand it many years later after reading internet articles) and I agree it's objectively unclear and can end being full of plot wholes for an average gamer
But still, we can't just ignore all the subjective elements that compose a piece of media like games, because the subjective side is exactly where are the most important key elements of any game. If we start studying about game design, you will see there are very few guidelines of how to make a good game design
Instead that are exemples of why people think games X or Y have a good design and then essays explaining why the author think the game design is good or why such game design worked with a specific demographic of players. This is the subjective nature of video games in making, because the answer will fall into the personal preferences of people who enjoyed the said "well defined" games