. . . "Clever" can mean several things, such as intellectual capability, or intuitive shrewdness, or wit and charm. Marianne seems to be quite well-read and articulate, but as she is still very young she lacks emotional "cleverness," i.e. sound judgment that comes from experience. For whatever reason, Elinor has that kind of good judgment without being very much older than Marianne.

For comparison purposes, think of how Hermione Granger uses the term in the first Harry Potter novel when she and Harry are talking about her capabilities, something like the lines of, "Books . . . cleverness . . . there are more important things, like friendship and bravery . . ." Hermione's "cleverness" is being a good student, absorbing her textbooks like a sponge, etc. I'd say something similar is going on with Marianne here. Time and experience will give her what she lacks.