The same pet peeves are common for so many people and I definitely share a few of them (no shopping cart at Ables, one ticket prints at a time, no bulk crafting, etc.)...
For me, one thing that kinda bugs me a bit is the music... it feels like the better songs all play at other times of day when I'm not playing. I work until 3pm everyday so the only music I typically get to listen to is from 3-6pm... once or twice I stayed up to 10 and 11 so I could get the beetles that are only around at 11.
My absolute favorite is the 12pm music, but I only get to enjoy it on weekends.