It's subjective. But one thing I think is pretty clear is that ToA invests a lot more into its storytelling and characters than Xenoblade does. Like, if you read interviews that Takahashi gives on Xenoblade he seems pretty down on his own game's story, like he wanted to put less focus on it compared to his previous games like Xenosaga and wasn't really trying to innovate (aside from the setting). Meanwhile, ToA has 518 optional skits and the like in addition to sidequests to develop both side and main characters. Xenoblades' heart to hearts are relatively infrequent and insubstantial and most of the sidequests I saw were for loot collecting or monster killing for NPCs with no role in the plot, not many for developing the side/main characters. I'm also pretty sure that ToA also has a higher cutscene:story ratio than Xenoblade since its plot is more complex and there is more dialogue despite being at least 20 hours shorter. One of the things that I didn't like about Xenoblade was that almost every time two characters talked to each other in the main story it was directly about the plot. The bare minimum time was spent on the human element, dealing with the characters' relationships and emotions. Heck, it's only mentioned a single time later on in the game that Dickson was the one who raised Shulk even though this has enormous implications on Shulk's backstory and on later plot twists.

Then there's the artistic message. ToA has so much to say about identity, finding a place in life, dealing with past mistakes, and learning to value yourself. What does Xenoblade have to say? Defy fate? Every other JRPG does that, usually as a side focus. It has no relevance to the human experience. I did like the relatively pacifistic message later on, but many other games do that much better, like Nier, Undertale, Spec Ops: The Line.

I'm not complaining about you in particular. It's just frustrating that Xenoblade's story will always be more popular than ToA's just because Shulk is a messiah whereas Luke is a flawed human. The writers did their job pretty well; you're supposed to not like Luke at first. It's essential to the plot and themes. But people act like the game is poorly written because of it rather than just recognizing that the game didn't fit their taste.