Tom, who was considered to be one of the greatest scientist s, w rote the book X. More so than "was considered", "had been considered" may suggest that he was no longer so considered after he wrote the book. With "had been considered" (especially) I would be tempted to delete "to be" to remove the faintly awkward or verbose-seeming "had been ...
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GPY"had been considered" may suggest that he was no longer so considered after he wrote the book.Thanks for your opinion.