I personally prefer working with Mods because when you're committing to an open source project because you're somehow limited with the owner of the projects goals.
They have a set of features that need to be implemented, and sometimes there's little room for innovations or ideas.
I find it more interesting when I'm allowed to mod a game because I can come up with my own version of the game using that engine, and if you provide an easy way to script my mods (LUA for example) even better.
For example, when I was a kid I always loved to recreate the american revolution in the starcraft universe.