I once studied the Apostle John's use of AUTOS in his first Epistle to see if one could discern how AUTOS is employed in 1 John 3:1-3 and other places throughout the first Johannine letter. One conclusion we can definitely reach is that AUTOS doesn't always refer to the nearest literary or contextual antecedent: the troublesome unit in 1 John 2:22-29 possibly demonstrates the seemingly obscure and varied Johannine use of pronominals. But with these facts in mind, I would like to take another look at 1 John 3:1-3.
Personally, along with R.E. Brown, I believe that these verses have reference to the Father. In 3:1, John recalls the love that the Father has shown Christians by bringing them forth as "children of God" (TEKNA QEOU). Therefore, God (the Father) is clearly the subject of verse 1 and John appears to continue developing this theme in 3:2 when he again reveals the status of spirit-begotten believers and their being recognized as "children of God."
What may of course seem problematic is John's use of FANERWQHi in 1 John 3:2 and his utilization of the verb in 2:28. 1 John 2:28 is evidently a reference to Jesus Christ and his royal PAROUSIA though I have often wondered whether it is really speaking of the Father (cf. 1 John 2:27). Leaving that problem aside for a minute, it appears safe to assert that even if FANERWQHi describes the manifestation of Christ in 2:28--God the Father is assuredly the subject in 3:1, 2.
D.E. Hiebert discusses the view of Westcott, that Christ is the subject of 1 John 3:1-2, before he poses some objections to this stance. Firstly, it's quite possible that 2:29 begins a new division of the missive. Regardless, one raises more exegetical problems by suggesting that Christ begets (spiritually) the TEKNA QEOU of 3:1-2. The verses in question (3:1-2) specifically mention the Father, and refer to those children of God. 1 John 3:9 makes a similar point and Hiebert even cites the Gospel of John 3:8 in order to demonstrate that Christians are children of God, "born of the spirit," but they are not born of Christ. See D.E. Hiebert, "An Exposition of 1 John 2:29-3:12," Bibliotheca Sacra 146(1989): 198-216. Compare 1 Peter 1:3, 23.
It may also appear problematic to speak of Christians one day being like and seeing God: "Beloved, we are God's children now, and what we will be has not yet appeared; but we know that when he appears we shall be like him, because we shall see him as he is" (ESV). But Jesus made a similar promise in Matthew 5:8 and John also writes that the anointed conquerors who will rule as kings and priests in the city of New Jerusalem will see God's face (Revelation 22:1-5). Furthermore, 1 Corinthians 15:49 promises that those who are privileged to live immortally and incorruptibly in the heavens of God's presence will bear the image of Jesus Christ (who bears and is the image--the express reproduction--of God's very being). So there is no difficulty in saying Christians will be like God, for there will be a number of ways in which they will always be unlike Him.