I was thinking in terms of biological evolution. I agree that evolutionary psychology and the rest are less robust. Regarding the origins of sense organs and nervous systems my understanding is that, although they may be quite detailed, these explanations are generally proofs of concept rather than precise descriptions. As to abiogenisis I don't know of any theory that has gained widespead acceptance."Yet is unquestioned by experts?" I am tempted to say their own theories - there are a great many DrKittens in science. However, to be more serious, I would say most of the subject matter of evolutionary psychology, (excepting my own work on sexuality and humour) most of social evolution (including all of memetics), most ideas about the origins of sense organs and nervous systems and all theories about the origin of life - apart my own work.
It seems to me that there's room for some parts of evolutionary theory to be less compelling than other parts without becoming mere handwaving.Really, the only evolutionary fields in which I find the reasoning and supportive data compelling are those that concern the relatedness between species. There you have serious evidence from the correlations between sequence data, Linnaean classification, geology and biological functions. One could not deny the quality of those results but so much of the rest is handwaving and it can never be more than handwaving because evolutionary theory gives no guide - predictively, it is a very weak theory.
I take it that you mean that the gene should not be considered as the fundamental unit of selection, at least not to the exclusion of other factors. What factors do you think are being overlooked?The reasons for the weaknesses, as I said, I consider to be the erroneous construction that is placed on evolutionary theory itself. Evolutionary theory should be based on data, not genes, and should recognise all data pools, not just the data in DNA sequence. Construct it properly and I believe evolutionary theory would do better.