That aside, would you be able to tell me which scenes you missed?
I've played through Ember and Abby questlines first, they were quite easy to find iirc
Then I've visited the beach, had to talk to every person on the beach, but found everything there was to find. Though, would be convenient if the main characters were highlighted in some way because I clearly can't see the different between random NPC and quest NPC
Visited restaurant. Despite it saying 5/5 progress in diary I figured that there still was some unseen stuff, judging by gallery room, I didn't grind restaurant 'cause 5/5 threw me off
Found Earlette, wasn't easy (but not hard either), had to run through few locations until NPC I spoke to turned out to be Earlette. Once again, highlighting story NPCs would solve this problem. Don't remember if had any problems with questline itself
Found Betty by some miracle accident. Not sure if the tile you need to step on was highlighted at all, but I wasn't looking at the floor, just randomly stumbled upon it, specifically investigating location for Betty. The main problem here was that I knew there is someone called "Betty" but had no idea where to look for her, so I didn't even know what location to start with, just figured I didn't find anyone there yet
With Jun the only thing that helped me was his sign next to the door. It told me where to look for him and I swear, for the very first quest (second, actually), I did check the area to the left multiple times and he wasn't there, until I looked at the sign and it told me to check there once again. For the rest of the storyline I just checked the sign or Jun specifically told me where to meet him, so sign for the rescue. I did miss these secret scenes with him tho, it's true.
For the Groupers, I knew what location they should be on and randomly found all 3 events quite easily, but I believe I missed the first one because I used the spray. Also not sure if finding them is easy or I was just so lucky, especially with the third event
So, to summarize, I had to check diary and search through every location to find NPCs I didn't yet start quest with. And I think highlighting quest NPCs in any way (making sprites more visible, literally highlighting, adding exclamation mark above their heads) would help A LOT
You could also consider making some hint menu in the diary maybe, that shows where to look for specific NPC at the current point of progression? Sounds like you should already have some variables to track such progression (those numbers in diary for example), so you could just add text to them hinting on where to go
