Hi Lucy,
I think what you are missing here is a few things. Firstly comparative morphology is not subjective in nature and can tell us a lot about biological organisms.
Secondly, as someone else points out, you seem to want to pit morphology against genetics. There is no need to do this. We can construct trees based on DNA, RNA, proteins, morphology etc. --And test these trees against each other. Thus, this provides another form of predictions that we can test using science.
And importantly, what we see from phylogenetics is a vast amount of evidence that agrees with each other for common ancestry.
To tie that into the original topic (and as a few pointed out above), this creates a large problem for the "evolution responsible for life after the flood" hypothesis. Because, we see nothing from genetic studies that indicate the severity of bottlenecking that would have occurred from 2 or 7 individuals producing extant populations (not that 2 or 7 individuals is even possible to sustain a population.
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