My suggestion would be to look at bikes with Women Specific Designs (WSD). Trek, Specialized, Giant (and a few others) should have something that your wife would want. Have her go out and ride a few to see what she is most comfortable on.

Since she is the one riding, she would be the best judge of what she likes and what feels the best. What bikes did your wife test ride that she had toe overlap issues on or felt the geometry didn't suit her so we don't recommend those?