>By vaccinating against these diseases, I think we are weakening the immune system.
Vaccination has basically the same effect on the immune system as fighting off the virus naturally. Normally, the body studies the smashed-up debris from the war against a pathogen and learns to recognize it. With vaccination, some already smashed-up debris are injected and the body studies it the same way.
I think the problem with vaccines is the simply quantity and diversity that is injected all at once. The dosage used during safety testing involving grown adults should not be used for a small child. Also the MMR vaccines combines three separate vaccines for no other reason I know of than convenience. I think it would be safer to do them one at a time at least a month apart.
A side effect of all this debris floating around in the body, either from natural infection or vaccine, is fever. It gets into the body's thermostat and messes things up. So it stands to reason that excessive amounts of vaccine can lead to high fever. And high fever is know to have neurological consequences for small children.
I suspect the problem lies in simply the quantity of vaccine.