Of course similar mutations are not necessarily a problem. Remember that we are generally talking about similarities in the phenotype, and ones that have functional advantages that are difficult to obtain in other ways. Your argument manages to ignore the role of selection and as such is clearly invalid.
Your example of the spiny teleosts and the Cypriniformes does not show that my state,ment is false - that is a logical error. Since my statement expressly allows for exceptions you need a large number of examples to refute it - and you do not even go into enough detail to be certain that your example is valid.
And of course there is no problem with transitional fossils above species level being relatively common compared to transitionals between species. It is even a prediction of Punctuated Equilibria. Punctuated Equilibria states that species tend to last a considerable time (even in geologial terms), yet transitions between species are take place in very small populations that are geographically localised over a geologically brief period of time (mere thousands of years). So it is not surprising that we should find fossils of species representing transitions between higher taxonomic ranks while intermediates between species should be rare.
Moreover we should remember that it is the transitions between higher taxonomic levels that are most problematic to creationism. Creationism can accept limited evolution between similar species. However we have transitionals representing larger scale evolutionary steps that creationists deny. Evolutionary theory states that these should exist - therefore the fact that they do is significant evidence for evolution which predicts that they would exist and creationism in which they are at best unexpected.