I share your preferences, but it's a rock and a hard place. Performing any of the tasks you listed by hand is extremely labour-intensive. Doing without those features is a harsh creative limitation - in my experience, the result isn't "this game feels retro", but instead "this game feels oddly flat, repetitive and static", which is much less forgivable.

I've worked on a game which aimed for authentically retro pixel art, but in hindsight I think it was a silly misallocation of resources. There's a reason it's so uncommon nowadays. If I were to try again, I'd at least include high-resolution 2D transforms in the engine, and possibly dynamic lighting too.

I briefly explored the possibility of developing a style-preserving realtime rotation algorithm for sprites, but it's a hard problem.