Actually it is a very good question and many webmasters ask about it so it is good to have a topic dedicated to it 🙂
Originally, the PHP standalone script had more features, now they are pretty much equal. The WP plugin is easier to manage and you can install different plugins to it and if you use WordPress and it is much more newbie friendly.
If you want to run big sites with lots of traffic, then it makes sense to use the Roboscript as it is more suited for this but if their plugin is very good and it is the way to go if you are starting out as an adult affiliate now.
Please do not forget to use my links to get anything from RoboScript and if you plan to buy some hosting, I have recommended some in my posts 🙂