Certainly we do not know what an atom or electron is really like. We just have various models that approximate the behaviour. Some models work better in some circumstances and not in others.
Are theoretical predictions really failing to produce experimental results?
There are certainly predicted effects that have produced results; the most obvious one is the Higgs, although the predicted search paramenters were very fuzzy.
A few others I found;The Kondo effect.
Thank you Max, you made me have to think.
My problem with alternative theories is that there are hundreds of them from loan cranks sitting in their basement to super smart researchers like Edward Witten and Sabrina Pasterski.
The fans of these theories demand that you must read and study the entire works of their hero; Randell Mills, Garrett Lisi, Rossi etc etc.
Luckily I am too stupid to be able to attempt to do this, knowing my level of stupidity saves me a lot of time.
As a tax payer I pony up the money for clever physicists to waste their time on string theory or whatever.
Presumably the theory that supercedes the Standard Model will be one theory that explains more phenomenon. So that would be one theory then!
Of course there is no guarantee that any of the current theories on offer is the correct one. We may have to wait another hundred years.
Or maybe nature is not as mathematically elegant as most physicists would like to imagine.