As much as I want to say that the focus was kind of on "The Ones Who Came Before" (i.e., the "ghost-lady" things you mention in this article) became the focus as soon as they were introduced in Assassins Creed II, (with the whole "solar flare" thing just a disaster both they and the rest of humanity wanted to see fixed) and that long-running franchises aren't inherently bad, I do agree that there's decidedly little developing in the "modern" world in comparison to all that goes on within the historical sections of the Animus. But I think the real problem isn't that franchises are designed with no end in mind - the stories in comic books issues, TV episodes, and video game franchises usually have self-contained beginnings, middles, and ends, even if it IS just part of a beginning, part of a middle, or part of an end for the overall story. The problem with the modern Assassins era is that it's relying too much on the self-contained stories of the historical settings, and doesn't put in enough effort to give self-contained stories for the modern era, stretching it out too much over the game series.
At the very least, some definitive action would be appreciated, and the few Desmond levels in Assassins Creed III were one of the few right steps for the game, giving our protagonist something to do other than simply see what his ancestors did, and doing some things of his own - even if it's doing them blandly, but it's DOING SOMETHING!!!
As for the whole bit with "look what happened when they 'ended' the Mass Effect series", it wasn't an issue of it coming to an end so much as it was having the original ending so full of plot holes and cliffhangers that it wasn't an ending at all, but a big fat neon sign saying " SEE THE REAL ENDING BY BUYING OUR DLC!!!" Even when the Director's Cut tied off most of the plotholes, it still seems to be setting up some other story beyond the events of Mass Effect 3. The only hope I have is that they at least advance time in the ME-verse far enough that changes are readily abundant, and that a new saga can be somewhat separated from the first three Mass Effect games.
Edit:
As for your opinions of franchises being bad because they don't wrap a story up in one, go, I think it would be best for you to see you fellow Escapist journalist Movie Bob's "Intermission: Franchise Movie DOs and DON'Ts" - even though it's about franchise movies instead of franchise games, I still think many of the lessons apply, such as "DO: Lay the groundwork for sequels. DON'T: Screw up the current movie (game) to do so." and "DO: Save some stuff for later. DON'T: Save EVERYTHING for later." The "Modern Era" of the AssCreed-verse definitely suffers from relying too much on the historical eras to set up sequels (rather than set up what's going on in it's own time), and also saving too many things in the Modern Era for some vague final showdown with the evil "Those Who Came Before"/ghost people, and leaving too much of the action that does happen completely offscreen. Assuming the series starts to give more development for the Modern Era, and also give a lot more for the player to do during that time, hopefully it'll mean the AssCreed story will be getting on track again.
