So much to go at here...
Define natural. Aspirin is derived from willow bark, is that a "natural" remedy?
Because a treatment worked for you, or your wife or even both of you, does that mean it is proven? No. Do you know that you would have caught flu without it? No. Correlation is not causation.
"what has been around for so long is now labelled 'alternative' as opposed to the medical breakthroughs that have come about in the last 100 years or so" - I'm not so sure. I would suggest that it's the stuff that is tested and that fails those tests which is labelled 'alternative'.
Please, please, please don't throw aspersions on vaccination, unless you have some very concrete evidence - just listing some potentially iffy ingredients in no way invalidates the enormous, in fact enormously enormous improvements in public health they have delivered. Look at the damage Andrew Wakefield caused and the recent growth in diseases that were previously considered beaten like mumps and measles. People who spread unjustified rumours about vaccination need to understand their responsibility for the damage it causes to children and think carefully before doing it.
I can't see the link between your overriding point about taking personal responsibility for one's own health and alternative medicine. Yes, absolutely educate and treat yourself before calling on our creaking health service, but it's irrelevant whether the treatment you choose is "natural" or not, what matters is if it's effective.
Run out of time, but I could go on and on ...