Nice to hear that you are planning to start doing a new one. This is something from the book The Mythical Man-Month it states that when doing software you should plan for a throw away version, the first version that you ever do which is kind of what you are doing and what I have come across in my personal plug-in project for Reaper. But for all of those throw aways and unfinished panels how about if there were some dumpster for them? Place where you could leave them and people should be aware by the context where they are available that they are what they are, no guarantees, only there to some one to pick a project up or to learn from.
From those choices the third one sounds best. The first one is good if you want to save the patch for later access, good for playing around with sounds.
The second choice is also very good because for some the workflow would contain the patches in the project file. You know when you are working on a track you can just open it and you get all the sounds from that.
So giving the option to choose from one from the other would be eventually most ideal in my opinion. But starting out with the first option, to get something saved, is better than not really working version of the two.
I think this idea taken from API design also applies here: It is easier to add something later than to remove something.
So do one version first and forget about the other options. Add other options when you have the time.
Ramblings about things related to the studio:
http://studio.therobotinitiative.com