I think JAST should work with MangaGamer to create a Steam like store for Visual Novels. Having everything in one place would not only make things easier for your old fans but would also make it easier for new people to discover the the community.
For this to be successful I think JAST needs to work with MangaGamer and make some kind of agreement that both JAST and MangaGamer get the full profits from their games wile splitting the cut for third party VNs, otherwise I doubt that either of you would be willing to joint the store of the other. Also since JAST and MangaGamer are the two biggest VN publishers in the west and if you were to work on this together other companies would be more likely to join your store over Nutakus or someone else's since your guys are more known in the VN community and would probably have more users then the others.
Also my personal opinion on this is that I would rather support a store you guys create then Nutaku or someone else especially since this way you would get to keep the full profits instead of giving a cut to the store owners. So what do you think everyone ?