that's fair. How would you handle it then? my initial idea was that the Skywalker in this story had a falling out and left the order, so they have to go find him/her (for me it'd be her)
One potential angle is to examine the consequences of Luke's chocies in the post-RotJ EU (I'm assuming pre-NJO, since if you're doing an 'outside threat' saga set in the further future, you're presumably nixing the NJO series first). This means we're mostly looking at the '90s EU, which was pre-prequels, and therefore didn't have a rigid conception of the Jedi Order.
That has interesting effects. Luke accepted Dathomirian witches and all sorts of people into his order, and the whole thing seemed much more loose than what we got in the prequels. Back then, writers seem to have imagined the Jedi Order as being mostly a training institution. You get taught how to be a Jedi by the wie masters... and then you go out into the galaxy and you're a Jedi. But, like Luke, you can be a Jedi and also a general. Or a policeman. Or a doctor. Et cetera. "Jedi" wasn't really seen as "
full-time member of a monastic order" but more as "
person thoroughly trained in the ways of the Force, and imbued with the noble values of the Jedi tradition".
Extrapolate from that for a few centuries, and there may be a galaxy with multiple "schools" of Jedi, influenced by various outside influences that Jedi took into the order, and by various interpretations of the Force. They all still agree on the basic tenets, and they all see themselves as Jedi, but some really are monks, others are pacifists who spend their time healing the ill and aiding the poor, others are like bands of roaming samurai (some seeking out injustices, others... more mercenary in outlook, and asking for at least
some pay). Some have turned to rigid traditions and stringently uphold the "no attachments" rule, others eagerly celbrate marriage and family.
This all fits very well into a galaxy that has been at peace, that has little centralised government, and that is not very ready (or willing) to whip itself into a coherent fighting shape.
And the Skywalkers? Take a leaf from the sequels; that idea was orginally from Lucas: "Skywalker has vanished". But in this case, it really makes some sense. At the outset, Luke and his immediate heirs believed in "let all ideas have their say", and this did indeed enrich the galaxy. But over time, it has dissolved a lot of (perhaps
too much) unity. And an uncertainty crept in. The lineage of the Skywalkers withdrew, and is now believed by most to have died out (at least in the main line).
But it hasn't. The Skywalkers still live, in secret, in hiding -- waiting for a time they knew would come.
(Have they removed themelves to give the galaxy the freedom to choose its own course, free from the all-to-powerful Skywalker name weighing in? Or have they set out to prepare for darker times in a hidden location? Many angles to take with that sort of thing.)