Well, in the 6 minute preview she reacts to Asuka calling out for Shinji to help her. From inside her entry plug. Across the vacuum of space... Yea, I have no idea what we're supposed to make of that one. I suppose the simplest explanation is that there's still some form of radio receiver in Unit 01 and Asuka was broadcasting on known channels?
The thing with Yui is that she's apparently a step above Gendo. If Seele are masters at manipulation, and Gendo's a step above them, able to manipulate their manipulations to fit his scheme, then Yui's a step above him. Not only is she able to play the game as it goes on, but she also had the foresight to anticipate the general style of moves some ~20 years in advance. Then again I suppose that part's easier than it seems since she has intimate knowledge of the relevant parties that we don't. She knows Gendo better than anyone, and if her relationship with Seele is the same as NGE she knows Seele pretty damn well too, surely better than we do. But I wonder how Wille factors into her plans? Did she anticipate that? Gendo apparently did.
Another question is how involved was she in Eva 01's actions at the end of 2.xx? Was 3I her goal or, anticipating Kaworu, was 3I just a stepping stone to her true goal? Was she involved in it? Maybe it was somehow an automated reaction (Or, of course, to be fair, maybe it was Shinji's doing. I'll present that as possible since this thread isn't about him.)
She's just... in the end I wouldn't even know where to start speculating about her motives. If they aren't the same as they were in NGE, which is a safe bet, then they're indecipherable to me.