Its not the fact that its from Microsoft, its the fact that both FAT and PE are full of legacy cruft that is no less painful than going through real mode in the first place.
Meanwhile ext family, even in ext4, requires that you handle optimizations decisions made for Fujitsu Eagle and its contemporaries.
I could easily read NTFS with hexeditor, calculator and pen&paper. Trivial even (most annoying part was the run length packing in 4-bit nibbles).
I gave up trying to read ext's cylinder-oriented mappings.
And FWIW, everyone has a read/write driver for FAT with LFN (and UEFI generally avoids names outside 8.3 just in case), using a different filesystem would lead to issues with OS support.
PE itself isn't really that much of legacy cruft, especially as far as it is used in UEFI (sure, you have the "program not for MS-DOS header", but that's useful for the rare case someone tries to open it under FreeDOS).
FAT originally only can do 8.3 filenames, but take a look at this to see what they hacked on top: https://en.wikipedia.org/wiki/Design_of_the_FAT_file_system#...
This is all the legacy shit you now have to implement when you want a so-called "legacy-free" boot. Infuriating.