This is what im afraid of, i like to own the full story, in this case the HD remixes were perfect, even the important story parts of otherwise unimportant games (358/2 days, Re:coded).
Heck, even coded was "just" a mobile game, but its very important to know, that memories of Ven and the others are in Soras heart, and that thats the reason mickey writes him a letter, which ties heavily into 3D. What im trying to say is, it was very good to make the App into a all time accesable game, for plots sake.
For me it would be a shame, because, in BBS Xehanort talks about a "Special Light" from the ancient Keyblade War, and Eraqus even tries to kill ventus... If in KH3 it would just be stated somewhere/by anyone that ventus is from the time the (first?) Keyblade War raged, without further pointing out the story of the Dandelions and Lauriam (most likely the complete Marluxia) it would SUCK to have to go on Youtube and watch the scenes of a Smartphone-Game. This is a Major Plot point, this is why Xehanort was obsessed with Ven, and created Vanitas (hopefully one of the true organisation).
Fans who followed the whole story from every game would be devided: those who played the app and know ventus past before BBS, and those who think he's just a random boy xehanort picked up somewhere.
Further, imagine, what if all the servers of the app would be shut down, and all videos from Youtube about it would disappear, and in KH3 in Ventus character entry would be written to play KHUx to know his whole story, what then.
You can imagine how much hatred i have for this app , of course not for those who play it, im playing too for the plot, but just because you cant put it onto your shelf to have the complete story accesable all-time. I just HOPE Ephemer won't be forgotten.
I have started the series with KH2 and absolutely loved it, without knowing about CoM and KH1, I am sure KH3 will be playable without knowledge of KHUx... you can play ANY kingdom hearts game without nowing about the others...... I am someone who plays Games (with actual Plot) more than once so if I start the kingdom hearts series again, i want to see everything, which i can, except KHUx. So just make a second pre-bbs Movie, Nomura, PLEEASE