"Roots are usually brown."
Translation:שורשים הם בדרך כלל חומים.
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Because of you omit it, the rest of the sentence looks like an adjectival phrase, as in "roots, usually brown."
If you do this then I would ask what it was about these usually brown roots that you wanted to say.
Put another way, the בדרך כלל here is an adverb modifying חומים. If we omit it we're left with שורשים חומים. That's just a noun with an attached adjective. It's not a complete sentence.