Alter the vaccine schedule.
1. Regardless of genetic vulnerabilities I think giving the flu shot to pregnant women, babies, and young children is a bad idea based on this CDC study that found that among males, increased prenatal exposure to thimerosal was associated with, "poorer performance with attention and executive functioning" Here There was a large increase in the autism percentage rate when the flu shot was first recommended for pregnant women. 
2. Also, the FDA set a limit of 25 mcg for injectable solutions because aluminum was causing neurological delays in preemies, so WHY is the 250 mcg Hep B vaccine given to all newborns INCLUDING premature babies?? This study found that "Low birth weight and preterm birth increase the risk of autism in infants by about twofold, but more so for girls than for boys".  Estrogen is believed to increase absorption of certain metals, which might explain why girls in this category would have a higher risk. (Babies born to mothers that are Hep B positive do NEED this vaccine, but most newborns do not.)
Vaccines contain dangerous ingredients, and therefore should only be given when clearly needed - just like antibiotics. Antibiotics used to be prescribed flippantly, but now we know overuse of antibiotics causes resistant strains of bacteria. So now doctors are strongly urged to only prescribe antibiotics when "clearly needed". Likewise, I believe vaccines should only be administered when the benefits clearly outweigh the risk. Here's a few suggested changes:
1. This study from the Harvard Cancer Center (here), found that having a health history of mumps parotitis actually decreases a woman's chance of developing ovarian cancer. So preventing girls from contracting the mumps could actually be increasing their risk of developing ovarian cancer. Since actually contracting the disease gives you life-long immunity and because mumps is such a mild disease for children I think the mumps vaccine should not be given to children. However, since mumps is dangerous for older males the vaccine should be given to pre-adolescent boys who have never had the mumps.
2. I think the Rotateq vaccine should NOT be on the mandated AAP schedule. In America, the benefits do not outweigh the risks of this vaccine. The 1998 version of this vaccine (Rotashield) caused severe intestinal damage and death (here). Also, it's a live-virus vaccine and I'm concerned this vaccine will actually cause more cases of rotavirus. There have been cases where children recently vaccinated against chicken pox actually caused an outbreak of chicken pox at their day care centers.
3. I also think the chicken pox vaccine should not be on the schedule either. It's a very mild disease for children but more difficult for adults. Unlike the actual disease, the vaccine does not provide lifelong immunity, and the vaccine even increases the risk of developing shingles. So children are better off actually catching the disease.
4. Since all babies and children are at risk of zinc deficiency, AND because they have immature immune, neurological, and renal systems, we should only give the most crucial shots to children under 2 years of age. Back in 1983, children only received 10 shots (for 7 diseases) by their 2nd birthday. Now in 2008 children are given 34 shots (for 14 diseases) by 2 years: Here. Think back to 1983. Did you hear about children in the U.S. dying from epidemics? On the other hand, now a child is diagnosed with autism every 20 minutes (72 kids every day), and almost everyone knows someone who has a child with autism. Additionally, we may not have childhood diseases anymore, but now children are suffering from significantly higher rates of severe food allergies, asthma, juvenile diabetes, cancer, and brain diseases like bi-polar disorder and ADHD. I'd rather have a temporary illness (such as the flu, mumps, chicken pox, or rotavirus), than any of those chronic lifelong diseases.
Everything has a toxic limit so we should not give our children 10,000 - 100,000 vaccines at once as Paul Offit has claimed would be fine.  Half of our children's vaccines contain more than 100 mcg of aluminum. Mulitply 100 mcg times 5,000 vaccines and you get 500,000 mcg of aluminum. (and 100 mcg times 50,000 vaccines = 5,000,000 mcg of aluminum!!) That cannot be safe. Remember, the FDA set a limit of 25 mcg for injectable medical solutions. If vaccines continue to be added to the childhood immunization schedule, eventually the amount of toxic ingredients in vaccines will be dangerous for all children -- even without a genetic susceptibility.
Disclaimer: Some vaccines are worth getting so ALWAYS consult with a doctor before making any medical decision.
I think we should "Green our vaccines", administer them at a slower schedule, REMOVE unncessary vaccines from the schedule (but they could still be available for parents who want them), and personally, I think we should also "Humane our vaccines". The means by which human fetal tissue was obtained for vaccine purposes is horrific, and unnecessary. Here. Regardless of your personal opinion of abortion, I'm sure we'd all agree that if a child is born alive as the result of a prostoglandin abortion, they should not have to endure this heinous attrocity: "50% of the time, the baby would be born alive, but that didn't stop them. They would just simply open up the abdomen of the baby with no anesthesia, and take out the liver and kidneys, etc."  I don't know if Merck or the other vaccine manufacturers will ever change their current vaccines, but a company named AVM biotechnologies has pledged to make ethical vaccines. Perhaps they could find a way to make them safer too? http://www.cogforlife.org/avm.htm