The Wachowskis definitely wanted to direct The Matrix.
The famous red pill/blue pill decision isn’t the only bit of color-coding happening in The Matrix.
The Wachowskis continued their relationship with the comic book medium in the years after The Matrix, with their Burlyman Entertainment comic company and their participation in the film adaptation of Alan Moore’s V for Vendetta.
A few months before making The Matrix, Keanu Reeves had a two level fusion surgery to repair two disks in his spine.