I actually kinda like how prominent she is, although it's making me wonder if my little headcanon about Yuu transitioning from Oldtype to Newtype is actually a thing with how it's presented. I guess it's just because of how vague it is.
That or its either those who didn't lose themselves (pilots not dying or going crazy after testing BD1 or the initial Blue Unit-0) as Marion tends to communicate with the pilots to set her free and they can see or hear her. In this case for the remake, we got Claire who didn't lose herself and heard Marion's words, while the initial pilots for BD1 in the SEGA game/SD Gen series/PS3-remake flatlined after fighting Kajima and the boys in their GM's during the introduction of the story.
It does remind me a bit with the SD Spirits version where he'd often hear Marion's voices in Stage 2 while using BD1 and Kajima (the first time he's got a CV, by Junichi Suwabe) wondering if the voices are from his head or he hears things randomly (but he figures it out halfway through the fight with Nimbus), he asks Alph of the system once they got back to space, and Marion talks to him after BD3's body drifts a bit before getting picked up by Alph and the gang.