It's possible to make a map of the holes in evolutionary theory - to see where other theories can be attached in order to provide support. That's the main function of this post.
The biggest hole in vanilla evolutionary theory is that it generally lacks a predictive theory explaining which creatures are fitter. For birds, the additional theories of aerodynamics are required; for bats, a theory of echolocation is needed - and so on. These other theories are more closely associated with developmental biology than they are with evolutionary theory. In general, additional theories that map from genomes to expected fitnesses are required.
Evolutionary theory includes or interfaces to genetics. Genetics also has some holes - or at least permits other modular theories to be attached to it. Genetics needs theories of mutation, merging and error correction. There are various types of mutation: point mutations, frameshift mutations, insertions, deletions and so on; mutational theories describe what can happen, when it can happen and how likely it is to happen. "Merging" theories cover recombination, symbiosis and rarer cases where genomes fuse or assimilate each other. A full theory theory must deal with mate selection - and the choice of symbiotic partners - since these factors determine which genomes merge. Error correction theories affect both mutation and merging. Genome modifications are post-processed by error detection and correction processes. These bias the results of these processes. Some modifications are permitted, others are rejected, and others are modified further. Error correction results in an adaptive bias to mutations - since the most deleterious mutations are selected against the most strongly by these mechanisms.
Some of the more vocal proponents of the basic idea in this post - that evolutionary theory contains holes - are Geoffrey Hodgson and Thorbjørn Knudsen. For example, in the paper: Why we need a generalized Darwinism, and why generalized Darwinism is not enough, these authors explain how evolutionary theories do not stand alone and depend on other bodies of knowledge. I agree with their perspective on this issue.