Let me just say up front that I am an autism researcher and have been on the front lines for years trying to educate parents about what is evidence based and what is fiction with respect to vaccines and autism. However because of working around scientists studying the maternal immune system and autism...I have wondered what is causing the increase in autoimmume diseases and allergies. So while those questions go unanswered at the moment....I am also a mother. When it came to vaccinating my children I have chosen to vaccinate but I am uncomfortable with the combination vaccinations. Are there any studies looking at long term outcomes of so many vaccines together? Eight years ago I spaced the shots out with my last child but got them all. Currently I am on sabbatical in Australia and I had a baby here, I declined the Hep B at birth and after going to the clinic at 8 weeks I found out they only carried the Infranix - Hexa, I got rotavirus for my son and declined the Hexa (DTaP, Polio, Hib, Hep B). I called around and found out that while I could not get the recommended vacs separated (a loth has changed in 8 years - or it is a US vs. OZ difference) so I went back to clinic and specifically asked for Infanrix-IPV (DTaP - Polio). The doctor ordered it and the nurse gave my baby the HEXA. I was so upset. I am looking for reassurance. I just cannot believe this has happened.
for what it's worth: my son (like at least half of European children) got vaccinated with Infanrix hexa and tolerated the shots extremely well (no temperature, no local reaction, nothing - he wasn't even grumpy - VERY different from DD after her DTwP/hib).
As for allergies, have a look at the hygiene hypothesis - essentially the idea that the lack of dirt and early exposure to a variety of bugs (very importantly, worms) make the immune system "bored" and react to "self" much more easily. A lot of available epidemiological data speaks for this hypothesis.
By "bugs" I meant germs and usually that happens through older siblings, early daycare, pets. Children who have older siblings, go to daycare early, grow up on a farm etc, do tend to have fewer allergies. As for the worm infections - same sort of thing. I recall them still going round in after school care when I was little, DD still had some once, but overall, hygiene and the fact that we are living in smaller groups is getting rid of the infections and allergies go up at the same time. Have a look here for example:
Exposure to other kids and the many trivial infections in the first year of life seem to be really important here (as much as they are going on our nerves ;) ).
As for worms, they are being used therapeutically, even - for example in Crohn's disease. My prediction would be that in 10 years or so, a round of worms will be part of the childhood "immunisation" schedule...