It doesn't take much to make a villain seem like a winner despite losing to the heroes.

A. They had a backup plan that the heroes didn't know about.

B. The plan the heroes foiled was merely a diversion from the real scheme.

C. The heroes did stop the scheme, but ceded something else the villain actually/also wanted in the process.

Just have the bad guy gain ground and he seems like a major threat. The fact that modern writers can't understand this shows how... basic they are.