Honestly the only real problem with the game is the speed/repetitiveness of the main gameplay loop. Sure I have complaints about the amount/variety of the content, but that's just 'I want more'. Aside from that, everything that makes the game annoying to play comes down to the speed with which you can do the main loop (without missing anything). Everything that annoys me (the lack of manual saving, hunting down the random events by going into shops, min/maxing credits by checking trashcans every day, etc) comes down to the fact that doing the 1-day loop takes like 5-20 minutes depending whether there's an infiltration and other stuff.
I think in general (with one exception) you can have a slow main gameplay loop as long as there's a lot of variety in it. If every day there was a new random shop event and different things happening on the streets or something like that, it wouldn't be as annoying to spend 10 minutes checking all the shops/trashcans every day.
The lack of manual saving is always going to be annoying if you have a slow gameplay loop, though. Fucking something up at the end of the day and having to re-do everything you just did is just unavoidably going to be annoying. I can understand wanting to make people's choices matter more by making it harder to save-scum, but you can do that well or you can do it badly. If you intentionally make the save-to-save loop long, you need to give people the information needed for them to make good choices. Using the infiltration system as an example - it incentivizes you to not rest (for better rewards) and to get to the end in one go (because it just resets to another infiltration next time). It also incentivizes you to retreat instead of losing. This is all fine, except that even normal fights vary wildly in difficulty based on sheer RNG. If I'm deciding 'do I do the next fight?' and all I know is 'there's like a 50% chance that the next fight is 4 mobs (which I will lose) and a 50% chance that it's 2 mobs (which I will win)' the choice isn't interesting, its just 'how much pain are you willing to go through for the chance of better rewards?'