I do agree that throwing all those shadows at you right after defeating Archangel is unfair, but none of the other things are, let alone "archaic". Designing your game so people have go use all the mechanics in it to successfully make it to a goal and adding penalties for failing in the process is a legitimate thing to do and adds tension and a need for strategy and caution.
Letting you retry after every fight would trivialize literally all obstacles in the game so might as well just make the dungeons corridors with healing stations every ten steps lol. There's always safety difficulty if you are more into that.
It's not that there shouldn't be penalties. It's at those penalty should be reasonable and consistent. I was OK with the penalties and persona 4 for example. However the amount of real world time it took to complete a floor in persona 4 is very different in the mound of time it takes to move from one safe room to another.
The difficulty also is not what matters. I do fine in at least 99% of fights on the normal difficulty. The checkpoint/save structure is not difficulty.
In facts the difficulty is easier than 4 and 3 in my opionion.
Having to backtrack to safe rooms because I simply want to take a break from playing isn't difficult. It's just unnecessary and lazy design.
The fights are fine. They give away the strategies to you more easily than the Rise scans in 4. The stealth is too easy, though the controls for t mhose particular mechanics aren't the best.
It's simply some quality of life design being poor.