From a bussiness standpoint of view, the old saga is a danger for the new one if we are talking about the newcomers, and the most dangerous game they could make is the 1999 one, if they make it "big" (for a HD console) i will seem too similar to the epilogue of LoS and many people will buy it thinking it is the continuation and then... all is screwed up because they will face the old complicated lore, and that's just from a story point of view, if it's 2D people will ask why is it different from the 3D LoS, if it's 3D, IGA will screw it up and it will be the end of the LoS saga and the old too (If this one is bad, why will they buy another 3D CV game? People won't differentiate who made it).
I don't know, but I petty much think the old saga is done if Konami wants to keep the LoS the "main one".
And consider Hideo Kojima is now Konami's vicepresident, and he has his money involved in the new saga, every game must be greenlighted by him and he probably won't like to risk his money... these are dark times indeed