I like the idea of VR training a lot. The ability is less "We're the only ones that do training together" and more "We're living in close proximity to each other, so it's easier for members of this particular group to train each other." How about...It's a combination of mundane training in addition to facilities that come with the ship? Like there's the VR thingy, maybe a gravity training room. But it's also possible for crew members to teach each other skills normally. That way, it can include stuff that can't be taught via brain upload, such as strength training or the ability to use magic.

And putting the ship as a character might be a good idea.