I think your sentiment is well-meaning but maybe a bit dangerous. It's setting up an unrealistic expectation of how adolescence "should" be, which risks leading parents to blame themselves or their kids when it doesn't turn out that way. Because it's extremely unlikely to turn out that way.
Adolescents are frequently at odds with their parents for the same reason 3 year olds are famous for temper tantrums: because it is part of the normal development of the human mind. Infants make no distinction between themselves and their parents; adults understand the difference completely. It takes about 18-20 years for that to develop, and there are well-known milestones along the way.
Teenage/parent conflict is certainly not a new phenomenon. You can find examples in stories almost as far back as there are records of stories.
> Conscious thought may deliver us to emotion, but the emotion that you arrive at is something that has always been inside of you.
Emotion precedes conscious thought; a big part of growing up is learning how to use conscious thought to identify, understand, and manage emotions. For very young children, emotion can be terrifying; it's great to feel happy but suddenly they might feel bad, angry, have scary thoughts, etc.--and it's all unexpected and unexplained. Teenage years are difficult because an entirely new set of powerful emotions, related to love and sex, emerge and the teenage conscious mind has to learn how to deal with them.
> What is the evolutionary advantage of making mothers miserable as a necessary part of producing offspring?
The answer to this obvious: to improve the fitness of the offspring. Conflict with parents happens during adolescence because adolescents are learning to how to be independent adults, and that means challenging authority.
Much respect to moms, but evolution does not give a shit about the mom once the offspring develops reproductive ability. Evolution does not give a shit about anything, really; I would not look to evolution to explain why people should be good to their moms.