Rather than it being a question of grammatical precision vs. colloquialism, or even of style, I think including or omitting the “in” is a matter of nuance. It seems to me, leaving it out of this construction expresses things in general or a basic state of affairs, but using “in” would mean to want a specific task done in a particular way (leading to the double entendre!)
If one uses “in” with “way,” it begs the question, why that way? It shifts the emphasis in the sentence to the verb. “She did it that way, [not I].” “She did it in that way [because it was easier].”
In any case, “want” or “prefer” are not driving the use of the word “in,” “way” is.
You do it your way, I’ll do it mine. Sinatra did it his way.

Hmm, I respectfully disagree, Kyle. I would say it's just the opposite; I can't think of any situation in regular conversation where a person can't use "common" as a replacement for "commonplace.” (Although I’m not clear on the distinction between spelling “commonplace” as one word or two. Also, according to the dictionary, there is an archaic meaning for “commonplace” that indicates a passage in a book used for reference.)

On the other hand, one cannot substitute "commonplace" for "common" when meaning something used or held jointly by more than one person. "The apartment building has a common garden" (used jointly by the tenants.) "Commonplace" in this sentence would suggest that the garden was unremarkable or lackluster. Likewise, "the two friends had common interests." Their interest could be in the Russian folk dances of the 18th Century, not a commonplace hobby.

Also, "common" can have the sense of being vulgar or coarse, as in, "All the people in the restaurant had their elbows on the table. It was so common!" If one were to substitute the word "commonplace" there, the sentence would imply that was an ordinary habit (perhaps of foreign culture, say.)

To me, the words are fully interchangeable for all the other senses. In addition to the more negative connotations of hackneyed or trite, “commonplace” shares the meaning of being prevalent, ordinary or ubiquitous. “While one rarely sees horses-drawn carriages in a big metropolis, in Central Park they are a commonplace sight.” Of course, one might argue that hackneys are hackneyed.