Prevents international use
One of the worst side-effects is that Verified by Visa makes international use of credit cards much harder. A relative of mine in the US tried to buy a train ticket in Peru - the company handling this turned out to be based in the UK, and required Verified by Visa. His US Visa card would not work. In the end we bought him the ticket, and he paid us back.
A little later I tried to buy an airline ticket from a US website, but they would only accept credit cards from the US, Canada, Australia, and the Phillipines. Apparently our cards are so much less secure than from these other countries. Once upon a time a Visa or Mastercard would work almost anywhere - but the system is breaking apart rapidly.