1. Stripe didn't exist 20 years ago. A merchant account was how you accepted credit cards online before Stripe.
2. Stripe costs more. I pay "interchange plus" which means a small markup over what Visa/MC/Amex charge to processors. A debit card can cost as little as 0.05% to charge, but Stripe will charge you 2.9%.
3. If Stripe goes out of business or decides they don't like my business, I'd lose my customers. Spreedly is a payment gateway agnostic credit card vault that lets me own the payment data and switch processors at will. If Stripe became cheaper or better in some way for me tomorrow, I could start billing my existing customers through Stripe tomorrow just by changing one token in my code.