Calling epigenetics a theory is like calling evoluton theory. There are numerous ways in which the function and development of an organism is affected not by the sequence of DNA but the epigenetic regulation.
See histone code, DNA methylation(especially gene imprinting), RNA interference as examples. You will have no changes in sequence but expression is totally different.
The support of epigenetic (above- genetic) comes from many elucidated molecular mechanisms that mediates epigenetic phenomena such as DNA methylation, histone modification, and miRNA. Each of the mechanism is responsible for inactivation of the gene ( gene silencing). It is not a theory. Until now there is not such a thing as objections.
I also have to mention that the Epigenetic changes play a great role in direct changes of the structure of the Genome and evolution. See attached paper
Article Epigenetic activation of genomic retrotransposons
At present there is no doubt on validity and the crucial role of epigenetics modifications on embryonic development, environmental adaptation, immune system and many others. There are plenty of reviews and papers on epigenetics, epigenetics inheritence, epigenethic therapy or diseases caused by epigenetics.
I am attaching our paper on transgenerational epigenetics. You can see how the parental treatment affects the DNA methylation and histone acetylation pattern across the generations.