Tiny necks are another reason I hate borrowing anything from Manga styles. Anime/Manga breaks a lot of rules when they want to, which any art style does, really; sometimes it's just harder for me to follow logically than western styles. Chibis like I used here are worse about it too, I don't think there's any universal rule for chibi proportions.
Not that it excuses the trouble I had placing the mouth, or anything you mentioned. I'll address them all before I get to the shading, thanks for the feedback.
Maybe I could avoid having skinny necks more easily by making them less tall as well. Even Freedom Planet characters have next to no necks for a reason, and Sonic Boom characters bury the necks they do have underneath clothing.