It’s occurred to me before (and I’m sure to someone thinking more seriously about it) that our way of categorizing organisms seems to be ultimately based on their origin, and not on something…more beneficial to the human experience, or more in-line with aesthetics and colors, or in some other way.

In other words, it is a deliberate choice to “taxonomize” organisms by their origins, and not by some other thing. This seems like an assumption that no one really questions, and I wonder if it ultimately leads to some unforeseen problems, or at least a view of the world that’s less than true or optimal for human flourishing.

You've got that exactly backwards. Humans say "fish" and "tree". That's the entire point of the article.

Ehhhh I strongly disagree with your statement.

The biological system of taxonomy is really for the biology of the organism. We have other categories we use (as humans who are not biologists), even though we borrow organizational structure from biologists! For example, the conceptual category of "vegetable" is a culinary term, not a biological one, and is a good example of a category not used by biologists.

There's a common saying, "Knowledge is knowing a tomato is a fruit. Wisdom is not putting it into a fruit salad". I believe that biologists should be categorizing organisms based on their origin, but people who are not biologists should not be bound by categories created by biologists.

For example, palm trees and bamboos are not trees biologically, but actually tall grass. The biological category of "tree" may not apply, but when you hire a landscraper, you aren't using the biological category of "tree", but rather the gardening category of "tree" (when you need a palm tree cut down). That's not a failure of biology, that's just because we use 1 word "tree" to describe 2 categories used by different fields.

Since an organism characteristics depend a lot on its evolutionary history, classifying organisms like that helps us make predictions and assumptions based on our knowledge of related organisms, so it's quite beneficial to humans. Also, the other classifications like tree, shrub, fruit, whatever, are also valid and used in biology, just not the main classification system. The other feature of phylogenetically classifying organisms is that it's valid for all life, which is a nice property.

Biology is fundamentally based on evolution, so when viewed through a biological lens, a classification based on evolution is appropriate.

We know of course that taxonomy is only one way to group organisms. People use plenty of others, including ones more beneficial to the human experience.

We group plants by the hardiness zones they can tolerate, for example. If you go to a plant shop they'll likely have plants which thrive best in sun outside, while others which need shade are inside or covered.

A zoo might group animals by where they are found, with zebras, ostriches, elephants, and giraffes together in the savanna section, rather than place all of the mammals together and the birds elsewhere.

As others already mentioned, "fruits" and "vegetables" are culinary definitions, not biological ones. Far more people use the culinary term "vegetable" to describe a tomato than the botanical term "fruit".

We also have religious classifications, like the Biblical prohibition: "“Nevertheless, these ye shall not eat of them that chew the cud, or of them that divide the cloven hoof: as the camel, and the hare, and the coney: for they chew the cud, but divide not the hoof; therefore they are unclean unto you.”