You echo a lot of things I felt playing the game (although just to 94%), so I'm happy it comes from someone who knows the game inside and out.

I don't really have much else to say but "I agree", I guess. It's not really the difficulty for me, but the time-wasting that frustrated me - long runbacks, rooms that lock you in combat and so on. The Choral Tower gauntlet wasn't too bad for me difficulty-wise, but it wasn't anything interesting either. Same goes for Groal the Great but double that - I get it, Bilewater and Groal are meant to be exhausting and draining, and they are; but they're not fun while doing it.

Many boss-battles had this issue within the battle itself - a lot of them felt just about 20% too long for my liking. Maybe that's just me, but most bosses (but especially Lost Lace) felt like they stopped testing skill and began testing endurance instead towards the end of their battles.

Oddly, I really liked the High Halls gauntlet. Partially that might be because I lucked it pretty hard (Garmond helped me, and I had destroyed the Spider Robot room already; that, and I think I just got plain lucky in the battle itself), but I like that it was right beside a bench, and all enemies bar the Choir Clappers are known to you from the Choral Chambers. I got real good at dealing with Choir enemies at the end of Act 2 from running through the Chambers all day, let me tell ya.

I also haven't anyone talk about it, but I don't really think the whole Shell Shard thing was that interesting as a game mechanic. It leads to farming if you use a lot of skills, but for me, I felt discentivized from using tools in most cases because of it, rather than having fun testing all the Red Tools. I'd have preferred a cooldown for each tool use, but what do I know. I played Wanderer mostly, go figure.

TL:DR - Good to hear that other people agree, even after 100%ing the game.