Like, I couldn't (or at least wouldn't) have gotten started on this project if I had to read the ATMega reference manuals from the very first step. But I did feel very frustrated that the Arduino "delayMicroseconds" function is so far off from accurate, and I felt frustrated also whenever I looked for deeper explanations of almost anything. It's a very copy-and-paste culture.
I eventually did find programming things more directly to be quite rewarding and worthwhile. My code is still in a ".ino" file, and uses some Arduino stuff, but it's basically built around ISRs in some frankencode middle state.
There's a lot of room for someone to create good tutorials and material for ramping up and out of Arduino. Would have helped me a lot, at least.