It seems I finally needed to write this out to actually decide. I'm going with the short stories. I actually like the web as it is now:
Blue: Origins storyline
Green: Pantheon storyline
Purple: Lessons storyline
Red: Second Chances storyline
All the Origins stories share the same theme (origins... like.. duh
) and can be read in any order, the Pantheon stories are seperate, but actually merge up into one story from Ariana's and Eolas's viewpoints, and everything leads into the Second Chances story.
The "Trial" story is a side story to Elani's, in which Koryna learns a hard lesson. It is sort of an extra, because I didn't want to leave the character of Koryna somewhat unfinished, as she is now in Elani's story.
The extremely cool thing is (in my opinion) is that you can actually start this web anywhere, read anything in any order, and converge into the main story; or you can start with the main story and spread outwards for more and more background information.
Damn. This brainthing will be a lot of writing.
Until in about 7 years or so...