My impression is that there is a mismatch between the usual proofs and justifications of God, and the nature of God.
(IMO) The main thing about God is that he is the creator, and that we live in a created reality. But modern people believe that creation is explained by physics - which makes God unnecessary.
But justifications and proofs of God (from Western Christians) are usually focused upon moral aspects - i.e. God is put forward as a guarantor of virtue; because modern Christianity has become almost wholly ethical.
Thus creation is seen as a matter of physics, while God is seen as a matter of morality; and there is no easy way of getting from physics to morals. It just doesn't make 'common sense'.
And if reality is explained by physics - then obviously there is no humanly-relevant purpose or meaning to reality. Reality is apparently all about cosmology, particle physics, relativity and quantum stuff... Reality is therefore explained-by forces, particles, waves, strings, proximate causes, statistics and things like that...
So God doesn't make common sense - to the modern mind. It is not so much that God has been falsified as that modern people just can't see the need or explanatory value of a God who is nearly always discussed in terms of ethics, morals, and virtues.
The answer? I don't see any alternative but to restore God as Creator and to emphasize that we live in a creation which has purpose, meaning, and coheres by relationships (not physics).
That is: Reality is coherent, and God as Creator is the source of that coherence.
That coherent reality is primary because created and being-created - and scientific truth, aesthetic beauty, and virtue/ morals/ ethics are just convenient sub-divisions of creation.
Some such metaphysical restructuring seems vital before modern Man can again know God.