-In general, a lot of non-combat related components can be better. Dragonrot can be improved, eavesdropping can be more prominent, grappling hook wouldn't hurt from a few more applications, etc. Nothing major but can really help in taking a next step in improving the flow of the game outside of combat.
-Story is simple which is fine, but for the components tied to the story (and by extension to side-quest stories) the pacing can be improved. Purification and Return could really have been more spread out throughout the game for its flags. Side-quests were generally lackluster: Samurai quest has too little interaction even though it spans the most areas, monk quest was fine with 3 possible splits but none of the three really made use of the character, doctor quest was too mundane as there is already a fetch quest in the merchant, the sister quest in palace also lacks interaction, and really it's more the great carp quest with interaction to the npcs being optional. I think pacing and utilization of quests in general would be my biggest complaint regarding the game.
-Enemy design was generally solid, but there is an issue with general design of counter exchange. This is expected considering this is really the first instance where the player has this much control over the flow of action. Specifically, enemy counter moves generally can be simplified to 'faster than player character's fastest attack', which is why looping is possible against all relevant enemy types (which is a large majority of them), and why while enemy moveset is sufficiently large and diverse, it's possible to not see a lot of moves and move transitions. First step to alleviate the issue is to expand counter moveset to beyond fast counter and super armour counter, which I have no doubt From will be able to do since several enemies already have a baseline for such design.
-Mikiri window is too large. This trivializes one type of attack entirely. This is really the only skill in the game that really counts as severe power creep to its other option (standard deflect) in my opinion. For something that already offers significant frame advantage and greater than normal posture damage (especially with the upgrade skill), the massive window seems like overkill.
-More generally, perilous attacks can be better integrated in various move transitions. Most perilous attacks currently only come after certain moves, attacks or attack chains, making it so that you know what's coming up to 5 seconds in advance, or that once a particular sequence is initiated that only one particular type is possible. In either case, it's possible to go on auto-pilot for a period of time that I believe is too long for the combat mechanic for the game.
-Not necessary an issue with the game, but I hope, if a future title is available, that aerial combat is integrated a bit more.
Most of the above are not really issues but more general, reasonable oversights, in that it's not at all plainly obvious on first encounter. Most of them are also easy and within reason to resolve, and given From's track record I look forward to how they will improve upon the existing design.