I think you are misinformed and miss the whole point of the article. Caffeine is not universally "bad". The research and data is clear.
Some ingredient in the coffee bean may have an antioxidant effect but coffee itself in it's natural form negates that because of the caffeine.
Based on what evidence? This is just a belief as I see it. The vast body of current evidence negates what you are saying.
If you have a genetic predisposition for diabetes, the caffeine in coffee will be worse for you than whatever good you get from the coffee bean.
Completely incorrect the research completely contradicts what you are saying. For one thing you are not taking the caffeine in isolation - the research relating to type 2 diabetes is quite clear and does not use decaffeinated coffee. This is the same attitude which has plagued previous research.
Right, coffee does have antioxidant effects, but caffeine has only negative effects. Show me one article where you can find any health benefit from caffeine. If you want double the risk of stroke, and lower insulin sensitivity (which is associated with aging) then go ahead and drink lots of caffeine.
I do provide sources so I don't base anything on mysticism. Decaffeinated coffee still has a bit of caffeine in it, even if not as much. This would mean there would probably still be a measurable impact on insulin sensitivity but maybe not as much. If you drink coffee at all, it probably should be decaffeinated coffee only. That way if you believe in the health benefits you can receive it, with the minimal amount of risk (caffeine). The more caffeine there is in your coffee, the more likely you are to reduce your insulin sensitivity, if you lose insulin sensitivity it may accelerate your aging. So to me it is pretty clear that caffeine is universally bad because it has no health benefits and is in coffee and while it may or may not negate the health effects of coffee, it would take a long term study to find out. I look at the stroke statistics, if the goal is good health and longevity, increasing the risk of stroke is not good, nor is increasing the risk of being diabetic which can take 15 years from your lifespan.
References
By the way, the source I cite keeps misinforming by confusing caffeine with coffee. Coffee has the health benefits and it's something in the bean itself .Caffeine has nothing to do with it as far as I can tell and seems to be associated with all the negative health aspects. Yet the medicalnewstoday article swaps "coffee" with "caffeine" for unknown reasons. I did find a benefit to long term memory from caffeine which is believable because it is a stimulant.
In my opinion, isolate whatever is good from coffee, separate it from the caffeine in the lab, and then sell the product in a pill. Then do a long term study which compares the pill takers to the coffee drinkers to see which group gets the most health benefits.
I would guess the pill would be better than straight coffee due to lower caffeine intake. I could be wrong.
References
http://www.medicalnewstoday.com/articles/270963.php
Again that is your belief. The research that I have cited uses caffeinated coffee. You seem to be starting with the assumption that caffeine is bad and looking at the research through that perception. That is not a good way to look at research.
Again I think you fail to understand how medical research is done. This kind of study would be ripped to pieces for poor methodology as taking a pill is quite different from drinking coffee. How would you know before the study what components to keep and what not to keep? How would the bioavailability and stability of the components compare when using an aqueous solution verses a pill?
It would be better to compare identical types of coffee except for the caffeine in order to do this. In that case you would need to ensure that the caffeine removal process did not change anything else about the coffee.
I'm sorry that's not research that's an editorial article.