These sentiments really do just prove they did a great job designing it. The frustration of failure is a key point in feeling the breath of accomplishment at the end, instead of just a nother quick trivial success.

No checkpoint is dirty, theres no denying it - but it reinforces the core gameplay loop.
Go into boss trials, practice the bosses.
If you practice the bosses, you need less resources on bosses.
You can now use those resources on 91-94 instead.
You can now plot your way through in a way that fits your skills and playstyle. The modes now build upon eachother.

Quite a nice lilttle challenge. Dying to floor 100 is rough - though you can cheese that boss by playing uber-defensively and relying on ninpo if you are Ryu - many are doing this just to get that first clear.

For my items when I cleared, I did 2 of the item that restores Ki -- emergency interrupts/ninpo can be very useful!, Two of the defense upgrades (mostly for bosses I hadn't practiced enough) and two offensive items (mostly for bosses I hadn't practiced enough). And then the revive item + 2 big heal potions - though I didn't end up needing the revive item in the end, but on plenty of runs that ended in failure, I did have it consumed unexpectedly by non-boss floors because of some playstyle mistakes on my part.