The main flaw is the large number of people who still continue to believe in his innocence even though the case proving his guilt is overwhelming.
From the point of view of the people who believe that he is innocent, the flaws would be as follows:
The DNA evidence: Hanratty's DNA and Valerie Storey's DNA were found on her underwear, proving that Hanratty was the rapist (and therefore also the murderer). But the different bits of clothing were stored together for decades before anyone knew about the technology of DNA, and it is claimed that they could have cross-contaminated each other. Rebuttal: (a) The techniques of analysis used are now so refined that it is possible to tell the difference between original primary DNA and secondary DNA from contamination. Even if the clothing had been rubbed together vigorously, it could not have produced the sort of DNA evidence which was found. (I do not understand the details of this claim, but that is what was stated by the scientists on a recent TV documentary). (b) No traces of DNA were found from another man, as would have happened if the murderer were someone other than Hanratty.
The Rhyl alibi: Numerous witnesses saw Hanratty in Rhyl in North Wales at times which would have not given him enough time to be in the Midlands where the murder was committed. Rebuttal: The times and descriptions given by the witnesses contradict each other, and in any case, the train timetable was such that Hanratty must have left Rhyl before the times when he was supposedly seen by the alibi witnesses - even according to the details of Hanratty's own statement.