2 Timothy 3:16 All scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness:
Every word in the Bible is true, but there are no words that state that Peter was ever in Rome.
The Second Epistle of Paul to Timothy is written by Paul from Rome - most likely just prior to his death at the hands of Nero. At the close of this letter, in Chapter 4, Paul speaks of those that left him, and those that are with him ("...only Luke is with me."). Nary a word about Peter. I infer that Peter was not in Rome at this time - and if Peter was ministering to the Jewish-Christian community in Babylon, that would fit the greeting found in the 2nd Letter of Peter.
Now its certainly possible that Peter went to Rome after Paul's death -- but scriptures are silent on that point.
The net of all this? It doesn't matter to me whether or not Peter ever made it to Rome. He was an Apostle of the Lord and we are blessed to be built upon the foundation that they provided, purchased by the blood of Christ, and made alive by the Spirit
Ephesians 2:19-22 Now therefore ye are no more strangers and foreigners, but fellowcitizens with the saints, and of the household of God; And are built upon the foundation of the apostles and prophets, Jesus Christ himself being the chief corner stone; In whom all the building fitly framed together groweth unto an holy temple in the Lord: In whom ye also are builded together for an habitation of God through the Spirit.
1) "Babylon" was used as a code word in the NT to represent Rome. This is well known -- so well known that it crops up throughout Protestantism. Here's just one example: http://www.armageddonbooks.com/226rev.html
"(3) That Rome was the city that was designated as Babylon. The Apocalypse would indicate that the churches would understand the symbolic reference, and it seems to have been so understood until the time of the Reformation. The denial of this position was in line with the effort to refute Peter's supposed connection with the Roman church. Ancient tradition, however, makes it seem quite probable that Peter did make a visit to Rome (see Lightfoot, Clement, II, 493 ff).
"Internal evidence helps to substantiate theory that Rome was the place from which the letter was written. Mark sends greetings (1 Pet 15:13), and we know he had been summoned to Rome by the apostle Paul (2 Tim 4:11). The whole passage, "She that is in Babylon, elect together with you, saluteth you," seems to be figurative, and that being true, it is natural that Babylon should have been used instead of Rome. The character of the letter as a whole would point to Rome as the place of writing. Ramsay thinks this book is impregnated with Roman thought beyond any other book in the Bible (see The Church in the Roman Empire, 286)."
"It is generally agreed that "Babylon" in 1 Peter 5:13 is a cipher for the city of Rome. The great city in Mesopotamia was no longer such in the first century. Diodorus of Sicily (56-36 BCE) writes: "As for the palaces and the other buildings, time has either entirely effaced them or left them in ruins; and in fact of Babylon itself but a small part is inhabited at this time, and most of the area within its walls is given over to agriculture." (2.9.9) Strabo, who died in 19 CE, writes: "The greater part of Babylon is so deserted that one would not hesitate to say . . . 'The Great City is a great desert'." (Geography 16.1.5) Also, no church other than Rome was claimed in ancient times to be the resting place of Peter. The Sibylline Oracles (5.143-168; 5.434), the Apocalypse of Baruch (10:1-3; 11:1; 67:7), 4 Ezra (3:1, 28, 31), and Revelation (14:8; 16:19; 17:5; 18:2-21) also refer to Rome as "Babylon." There was a reason for connecting the Babylonian and Roman empires, as Norman Perrin writes, "Rome is called Babylon because her forces, like those of Babylon at an earlier time, destroyed the temple and Jerusalem" (Jesus and the Language of the Kingdom, p. 58)."
It is only with the advent of Protestantism that some Christians began to routinely deny the commonly held belief that Peter had been in Rome.