Stupid question, did you check to make sure all your parenting was done properly? And sometimes if you check the bone roll settings (I don't know if it's still relevant with current version of Blender) and make sure it's 0 that used to be a thing that helped (but I don't know how or why).
Otherwise looks like your rig is coming along nicely :)
I learned exactly enough rigging to know how to do it and learn how much I hated it XD so I use rigify and modify it :)
At some stage when you're not concentrating on rigging check your polyflow around the hips/thighs and shoulders to help your deformations (hopefully you find it easier than I am, I'm still struggling a bit).
I think I got what you mean. I think such nuances are just practice and further attempts to make the animation better. At the moment, I do not strive for the ideal. I need a working prototype.
I decided not to use rigify yet because I need to learn how to animate everything I need. Not only humans and animals. Creatures, different enemies, mechanisms, etc.