Saying that the mechanisms are known is a major case of hubris. For example, it is still not known exactly how aluminum salts, used as adjuvants in vaccines, work. Many vaccines were developed empirically, and researchers struggle to replicate the success for other diseases. If the mechanisms, as you say, were fully known, we would already have conquered cancer.
Here is an interesting example. In the 60s a vaccine against chlamydia was developed and then tested in one of "developing" countries. Vaccinated people showed high titers of antibodies in their blood (this is, by the way, how efficacy of vaccines is judged, not by the actual clinical studies, read the inserts, you'd be surprised). Despite the high titers vaccinated people were much more likely to get the disease and the course of the disease was more severe. The vaccine was pulled, and the reason for the failure was not known at the time.
http://www.smithsonianmag.com/smartnews-science/why-1960s-ch...
If you follow the links in that article you will see how the process of how the body deals with a vaccine is not necessarily the same as the process of dealing with the disease directly.
Human immune system is complicated and is not fully understood. Infant immune system differs from the one of the adults, which further complicates the matters. Saying that the science there is settled is just not true.