My preferences tend in the same direction on this. I feel that the Vong were more 40K than SW, in a sense. An interesting idea, sure, but I'm not convinced they fit into the setting very well. (Although, to be fair to the NJO writers, them being really 'alien' was kind of the point.)
I also agree on that side of the Force, and this is also -- sort of -- where NJO actually ended up, what with Jacen's and Luke's ultimate conclusions on the matter in
The Unifying Force. On the other hand, I do despise the (memetic, game-dynamics-inspired) idea of "Grey Jedi" -- insofar as people take that to mean "half light, half dark, ALL edgy-and-cooler-than-thou".
As I've discussed on AH.com in the past, and in conversation with some others on this board, such as
@Earl, one option would be replacing the Vong with an external force (heh!) exploring that concept and its intricacies. A faction representing an ostensible "third way" approach to the Force. Which can then ultimately be deconstructed to illustrate how wrong that can go. (While also still leading Luke and the other Jedi to re-consider their own view, and causing them to arrive at much the same conclusion as we saw at the end of the NJO series.)
Then again, people less interested in deconstructing the "grey Jedi" meme might not be so enthralled by that, and in any case, I suggested it as a sort of "substitute" for the Vong. I'm not sure if I could make it work if we shift the context to "several centuries later".
That being said: I went with "infiltration of the Republic (and the Jedi)", because that's what NJO did originally, and also because it would show the "Third Way" philosophy being superficioally very attractive to many people. But you raise a fascinating alternative concept:
"[
A]n advanced society that can artificially create their own force users"
That really seems like something you could take into interesting places. Obviously, it can't be clones (we've had that idea already). But the notion of a faction that can use some -- presumably technological, or MagiTek -- method to
create Force-users would really be a game changer in the setting.