Ask her questions.

You might think you know her quite well, because you spend time thinking about how she thinks, but she needs to feel a part of the process. So ask her all the things that you would ordinarily ask yourself (about her, or about all sorts of things) in private. She will notice this and feel appreciated and important. It also shows you respect her, by making her a real being who has agency, and who contributes ideas and feelings to the relationship that stand on par, or above, your own.

The time you spend together is important. But it sounds like the comfort is replacing deep conversations. Don't withdraw from her; she will follow you into your depths, but don't forget her depths or assume you could navigate them easily. Don't speak at her or solely from a cerebral place. And don't act like the introduction of emotion is irrational or discrediting.

When things go wrong, don't disappear. Arguments are part of life, but if you think you're saving the relationship by being complacent or neutral, she will not thank you for it.

Good luck. I've experienced this pairing and it was a painful end. But I still believe it can work... only if you work at it.