Dilly, your experiences and observations show that individual outcomes cannot be predicted by looking at statistics. There is a lot of discussion on this in the MN archives, and the best studies on health outcomes of infant feeding do indeed take into account all the variables you list.
In your mother's case, I don't think there are any studies that show exclusive breastfeeding protects against late onset diabetes - the diabetes protection is against juvenile diabetes. Ditto obesity. It's obesity in childhood that's looked at.
The only way to get decent infant feeding statistics in a western context is to have huge samples, because western babies are protected against a lot of illnesses or serious consequences of illness simply by having access to good medical care and clean water, immunisation and so on however they are fed. You also need large samples as some of the outcomes are quite rare - chrons (sp) disease is more common in FF babies, but you need to get a lot of babies and compare them before it shows up.
Age of starting on solid food is also an issue, especially as formula fed babies start solids rather sooner than breastfed babies (according to the UK Infant Feeding surveys), so for some studies, you need to have this as a variable in some studies ie is this outcome a result of early solids, or formula feeding?
There are plenty of good studies that control for all this.
We don't know if modern formula would be different, because no one really looks at the long term differences before launching a new product - this is one of the drawbacks of formula being a primarily commercial field, where manufacturers are keen to get new formulations out there. The manufacturer who says 'no, let's wait 10 years and monitor this sample of 100 babies and see what's happened before we go into production with this new ingredient/addition' doesn't exist!
In fact, the independent work that has been done on the effects of modern formulas show that the health claims made for them don't stand up (see the reports on manufacturers claims for the benefits of prebiotics), not that they are likely to be more harmful than older formulas.
I don't agree with your argument which is basically 'my observations and my maternity nuses observations don't tally with the statistics. I know this proves nothing. It also shows that the research on health outcomes of different infant feeding regimes may prove nothing as well'.
Of course there are plenty of bad things a parent can do to a child whether they are breastfeeding or formula feeding!