First, my thanks to all who responded to my dilemma. Of the relatively small sample it was about evenly divided between those who preferred Series to Universe.
Personally I prefer a Series. Universes such as NiS are too big, making it hard to follow a set of stories like mine. Even going to the page of an author as prolific as Don Lockwood (34 stories, 7 in the NiS Universe) still makes it tough to string them together. Even sorting his page by story date the 6th and 7th stories appear before any of the others, and they are all interrupted by stories that have nothing to do with NiS.
Some respondents said that a Series CAN be included in a Universe, and pointed me to the relevant page of instructions for authors:
where it says "Through the universe management page, you can create a new universe, add a description for it and add existing stories OR SERIES to it." (emphasis mine)
There are even schematic diagrams which show a Series nested within a Universe.
There is nothing under "Series Management" that says anything about how to get a Series into a Universe.
We know as authors when we submit a story we CAN link it to a Series or a Universe, but can we do both at that time? I don't know, I've never tried and I don't have a story ready to experiment with.
Anyway, the implication is that only the creator (Author) can add a Series to their Universe. In my case there is no author listed for the Naked in School Universe, so there's no one I can ask to do it, and with the stories in the Universe I can't create the Series UNLESS I can remove them from the Universe. I haven't found a way to do that yet.
So here's the rub. When you submit a new story you CAN select a Universe for it, but once you do that you can't seem to get it out of it. When you create a Series you can't link that to a Universe, and once a story is in a Universe you can't create a Series for it, even if the stories are already in a Universe, as mine are.
The solution, it seems to me, is to give the author of a Series the same option he has when he submits a story -- let him pick the Universe he wants to link his Series to.
But then we encounter another issue -- what if his stories are NOT in that Universe? Just list the Series the same way you would a single story -- clicking on the link would bring up that Series.
However, if the stories are already in that Universe we create a double-listing, one for each story and one for the Series it belongs to. Unfortunate, but I don't think it is a deal breaker.
Stories that are in a Universe are linked to it. Stories that are in a Series are linked to it.
Question: Has anyone ever seen a story that is linked to both a Universe and a Series?