6s vs 3s tranny problem questions

Hi all,
Was all set to buy a used Mazda 3s for my daughter when she changed her mind and decided she'd rather have the 6s. She's used to driving an automatic, so that was going to be my first choice. But, now I'm reading about transmission problems with Mazda. Do both of these cars have transmission problems or is it just the Mazda 6, or is it just the auto? Does the manual transmission have less problems then the auto? Which model has less problems? Is there a year I should stay away from? I had a 1988 Mazda 626 turbo, 5spd that I bought new. That car ran for 200,000 miles with the original clutch and tranny!! I understand that the automatic tranny that year had all kinds of problems. Please advise. Thanks