4-5 years ago, the desktop application was probably what you wanted to use. Nowadays, the browser is an OS, and if it is not on the Internet, people simply will not use it. You get simplified deployment on the Internet, and anyone can access it anywhere. With WPF, do you get ... stronger gradients?
"I thought it was better to write all the controls in WPF instead of HTML, as it is probably even less likely to be used by hackers."
The intranet website will be as secure as the internal wpf application.
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