A Journal of Apologetics, Vol 1, 2010
“The phrase translated in the King James Version as “only begotten Son” is monogenes huios. However, one should not take this in a literal, physically paternal sense. […] The translation of monogenes as “only-begotten” is, in part, a result of the King James translators retaining Jerome's Latin translation of the term, unigenitus, meaning “only begotten”. However, the Latin text existing prior to Jerome's translation did not use the Latin unigenitus when describing God the Son; instead, it utilized the term unicus, meaning “only”. 
In order for the Greek manuscript to warrant the translation “only begotten” the Greek term being translated would need to be monogennetos. To translate monogenes as “only begotten” is, without question, less than precise…
Commenting on this […], James White noted that
The key element to remember in deriving the meaning of monogenes is this: it is a compound term, combining monos, meaning only, with a second term. Often it is assumed that the second term is gennasthai/gennao, to give birth, to beget. But note that this family of terms has two nu's, rather than a single nu, found in monogenes. This indicates that the second term is not gennasthai but gignesthai/ginmai, and the noun form, genos.
Additionally, William Mounce explains that monogenes can only be understood as stressing the unique nature of Christ, it cannot and should not be understood to imply any type of biological siring. 
This metaphorical understanding of sonship is demonstrated in the book of Hebrews. The author of Hebrews refers to Isaac as Abraham's “only begotten son” . Making use of the same term found in John 3:16 to describe the forther-to-son relationship (monogenes), the author of the Hebrews notes the unique nature of Isaac as the promised child from God. The Muslim reader will readily admit that Abraham had multiple children; therefore, the intent of the text is to stress that Isaac is Abraham's unique son, not his only son. 
Craig Keener believes the use of the term monogenes in John 3:16 is intended to call to mind the traditional Hebrew understanding of Isaac. Just as Abraham gave Isaac, God the Father has not given merely a son but the unique, beloved Son with whom there is no comparison . In the same manner, Christ should be understood as the unique, one-of-a-kind, “Son of God”, the Son of God as an equation with God rather than a statement of biological origin.
 “In the Cathedral of Vercelli, Italy, is the most notable of the Old Latin MSS, Codex Vercellensi(a), supposedly written in A.D. 365 by Eusebius, Bishop of Vercelli. In this document, which contains the Gospels, with Iacunae, the word monogenes in […] John 3:16, is translated with the Latin word unicus (only), not unigenitus (only begotten). Dale Moody, “God's Only Son: The Translation of John 3:16 in the Revised Standard Version” The Journal of Biblical Literature Vol. 72:4 (1953), 214