Everyone who habitually says “the way in which” is a pretentious fool. Nine times out of ten, this silly phrase can be replaced with “how”. The same is true for the plural version, “the ways in which”. If you ever really do need a concept of the way or ways that something has happened rather than simply how it has happened - which if you're the kind of twit who likes saying “the way in which” is unlikely, because it's improbable that you think sufficiently deeply to make such a distinction - then you can say "the way that" or "the ways that".
‘‘Habitual use of “the way in which” is the mark of a fool. There are no exceptions.I'll say one thing for the phrase, though. It marks someone's writing or talk as not worth the attention of those of us who value precision and clarity. I really enjoy reading what someone has written, or listening to them talk, when they know what they're writing or talking about and when they're issuing words because they want to help me feed my wish to understand, my desire to learn something from them. What I don't enjoy is listening to people who dress up their writing and speech with unnecessary phrases that carry no content and that don't assist with communication either. “The way in which” is an ugly and dispensable phrase which doesn't make a person sound knowledgeable or willing to impart their knowledge at all. It's equivalent to them asking "yah" or smacking their lips three times at the end of every sentence. It makes a person sound like an idiot - all role-playing and no care for real communication, for genuine intersubjectivity.
If you find that you've adopted this phrase, please drop it. It's never too late. Stop using it now.
If you're stubborn and you want to give me an example of a sentence in which “the way in which” is the clearest phrase to use - preferable to “how”, other alternatives, or recasting - email me and let me know what it is.