Just to keep things in order, in case anyone tries to read this blog straight through rather than jumping around, I'll insert a short note here that I've already analyzed the rest of Matthew 1 here, and Matthew 2 here (with verse 11 in particular addressed here). Merry Christmas and all that. So, on to chapter 3.
The first issue that the SAB has with this chapter is whether or not John baptized any Pharisees. I think this isn't a problem; in verse 11 I don't think John is addressing the Pharisees in particular, but the crowd at large and saying that baptism is something he's offering whether or not any particular member of the crowd is taking him up on the offer. As for calling them "O generation of vipers...", yes, I'd agree that this is harsh language, but I'd note that the word "generation" may be somewhat questionable in meaning, so I'm not sure what the SAB is insinuating about "an entire generation". He may not even be talking about the Pharisees as a whole.
I think marking verses 10-12 with violence may be a bit strong, but I don't have a major issue with this. The point that John is making is a metaphorical one. If a fruit tree doesn't bear fruit, then what good is it, and why not just use it for firewood? So if you're someone who isn't doing something worthwhile with their life, then what good are you? It's food for thought, in my opinion.
Now the SAB thinks that Jesus coming to John to get baptized is absurd, and as they note, John himself seems to be of the same opinion. It is rather odd, and for the very reasons that the SAB points out. If baptism is is about repentance and sinfulness, and Jesus is sinless, then what the heck is going on? I've heard it suggested that Jesus is getting baptized in order to be an example for generations of Christians to come, which might be possible, but I think that it's a mistake to assume that everything Jesus ever did was intended to be an example to follow. I suppose it does make some slight sense out of verse 15, of which the SAB wonders as to the meaning.
The last issue in this chapter is a question concerning the wording used by the voice of God, which here disagrees with the parallel accounts in Mark and Luke. Make what you want of this sort of thing; slight differences in wording in the Gospels don't bother me personally, and this is only the first of many of this sort. I figure if the gist of the wording is the same, why should it bother me?