I was going to call this DOS vs ProDOS, but I won’t argue the DOS side. I know that there are hundreds, possibly thousands of programs written for DOS.
By the time I bought my Apple //c, in December of 1984, ProDOS had been out for over a year. DOS had been out for over five years.
My Apple //c came with a set of diskettes in a neat little plastic case. They were designed to show off the Apple //c. I’m afraid they spoiled me. One of the diskettes was Getting Down to Basic which showed you how to write programs in AppleSoft Basic using ProDOS. Another diskette was the System Utilities diskette, which is based on ProDOS. So right from the start, they pointed you at ProDOS as your disk operating system. That is what I learned Applesoft on.
Later on, I ran into DOS. There is some great software written for DOS.
One of the most glaring differences to me was the lack of lower case support from DOS. By buying an Apple //c, I bought a machine easily capable of using both upper and lower case text and eighty columns. Both of which, I planned on using. DOS was written for Apple II’s that did not have eighty columns or lower case letters.
I know there are many who prefer DOS to ProDOS. I’m not one of them. I like the design of ProDOS. Most of my original books were on ProDOS. It was designed with larger disks and extensibility in mind.

Back in the day, I liked DOS better, Prodos just seemed needlessly complicated for what I thought it did (keep in mind I was in grade and middle school).
Today, prodos as much as possible thank you!
I grew up with DOS. When I came to PRODos, all the folder structure stuff seemed overkill, though it suddenly made sense when the disk size went from 140kb to 800kb or more. I still hate having to type disk prefixes at the prompt today, and try to avoid getting into that situation in the first place. The other thing that bugged me about PRODos was that you could get NO BUFFERS AVAILABLE errors trying to BRUN some games if you put them on PRODos disks. And I do like that you can type long, wacky file names in DOS!
But my concerns are pretty small fry, really. I leave binary game files on DOS 3.3 disks, which is where most of them came from. I try to avoid doing lots of typing of prefixes by doing that kind of thing with utilities. The hugest gains in PRODos for me are in Applesoft, and they alone are worth the price of admission. The STORE and RESTORE commands save you the hours it takes to write code to write and read text files. The automatic garbage collection is a zillion times as fast, and you don’t have to type ?CHR$(4) twice in a row (or equivalent hack) to issue disk commands like you did in DOS 3.3.
I feel super comfy in DOS 3.3, but I would never program there in BASIC anymore.