Alright, I've pretty much filled out the "flowchart" by this point. Well, I'm on track for the true end, and it's basically straight shooting from this point, so I suppose I can share some thoughts. The new character art is really quite good. The body shots have been replaced with headshots, but that's not too bad. The facial expressions are what matter most, and those are, again, good. Junpei now has new character art in-game which is also cool. My only gripe with this new "speech bubble" system is that the character faces still appear over CGs, even when those characters are IN the CG. I'm okay with other speaking characters getting "headshots" while those CGs are up I suppose, but seeing the same person's face appear on screen twice just felt sort of odd to me.
Also, the music looping was rather clumsily done. The way it seemed to work was that after the game would go through a loop of any particular track, after the loop finished, the next loop started for about half a second, but then the song reset and started ANOTHER new loop, which was a surefire way to yank me out of the experience.
Finally, a new...piece of story was added, but sadly, it honestly doesn't contribute much. Even so though, the ios port of 999 still spins a wonderful tale and is good for perhaps a revisiting of the story. I wouldn't use this port as the first time experiencing 999, however. Upon completing an ending, the game will flat out tell you which doors to go through for completion. Also, the flowchart model of story jumping sort of added complications to certain required story flags, and if you don't know to rewatch certain scenes, you can actually MISS entire scenes if you jump ahead. Keep that in mind if you plan to make the ios port your first run through.