He Wouldn't Have Had the Time
Proponents of the Baconian theory of authorship assume that Francis Bacon had the time to write the volumes of Shakespeare. He would have been far too busy in his work to pen the works attributed to Shakespeare.
He Was No Poet
Even a quick glance at Bacon's attempts to write poetry reveals the folly in believing he was the author of Shakespeare's plays and sonnets. While he could write prose and philosophical texts, his poetry was very weak and does not hold up in comparison to Shakespeare's sonnets.
There are several anatomical and scientific mistakes in Shakespeare's plays that Francis Bacon would not have made. Bacon was a learned scientist and would have understood the prevailing theories of science at the time.
For example, in a Midsummer Night's Dream, Shakespeare mentions, "certain stars shot madly from their spheres."
At the time, it was believed that only other planets, the sun and the moon were part of different spheres. The stars were believed to inhabit the same sphere as the earth. Bacon would have understood this and not made this error.
With a body of work as large as Shakespeare's, it is easy to fabricate and extrapolate any code of your choosing. When Baconians speak of hidden similarities and numerical cyphers, it says nothing more than with a sufficiently large body of work, it is possible to find a "code" or cypher that gives the desired yield.