Secondly, vaccinations generally work by stimulating immune response, so I don't think there is any real fear that we're compromising our ability to naturally fight disease because of vaccines. You may be confusing vaccines and antibiotics.
I'm not weighing in on whether or not this particular move by the CDC is valid. I'm still thinking about it. And as the father of a 6-month old I have seen my baby's screams as she receives four shots in less than 60 seconds---so I'm definitely an "interested" party. But I don't know, is the flu worth it? To be honest, the flu vaccine probably more appropriate a choice than the chicken pox vaccine---which by all accounts was recommended primarily for economic reasons, not health ones. At least the flu kills people, that's a defensible reason for using it. Still, it's not a slam-dunk like the polio vaccine. So is it worth it, statistically? I don't know.