The comically bad story, the lower quality of some of the chapters, escort missions, and awful QTEs count as flaws.
The vial system makes the beginning much easier for newcomers compared to the flask system, as you can have the maximum amount right from the start. I had some issues in DS3 with reaching the next shortcut/bonfire before depleting the supply of handful flasks.
Chalice dungeons were meant to be played while proceeding in the main game. Even the early ones posed a challenge, if you started them when you got access to the first after beating BSB. The later ones weren't unfairly difficult, more a test of patience, even the notorious Defiled one. Personally, I enjoyed their roguelikeness.
To my knowledge, you can make a pretty OP Bloodtinge and Arcade builds with gems. The latter is the only trait that improves beyond level 50.
Certain consumables not being restocked automatically, and not being able to transport without visiting Hunter's Dream were certainly minor flaws though.
