Best design for plugin to generate custom content on page template

My plugin goal is to display dynamic page content (calling other web services) and post forms as a regular wordpress page.

I have been successfully calling my plugin by using a shortcode in a page. It was all going fine, when I realized that with certain themes my plugin was called twice. Horrible! I saw that others had similar problem, and I have the feeling that my design is not correct: in the following, https://wordpress-hackers.1065353.n5.nabble.com/How-to-prevent-multiple-processing-of-shortcodes-td38391.html, Otto says that a shortcode is not meant to do things that have side effects, like posting data, mine is exactly doing that.

So should I continue to use my shortcode and use Otto’s init hook or should I change the design ?

Thanks !