Having a high-quality plotting tool is necessary for TinkerCell, so gnuplot seemed like the right choice. gnuplot has a scripting interface and can provide a large variety of graphs. The GnuplotTool plugin generates script files and pipes them into the gnuplot executable. So, the only work that is done is generating the scripts. The plugin also provides a scripting window where users can plot more advanced plots (anything allowed by gnuplot).
GnuplotTool and the default (old) Plot Tool provide the same functionality. When one has been loaded, the other cannot load. So, the one that loads first wins (this depends on which plugin was created first). Disabling one of these plugins from the settings menu would be ideal way to choose one of them.