I have been thinking about a 331 build and the advice I usually get is to go with the 331. If you do your research, a 331 short block is only a few hundred more than a 306 shorty. I have seen 306 sb from $1000-1600(forged pistons/cast cranks), and 331 from $1400-2100(forged pistons/cast crank, 331 with forged cranks from $2100-2500. Now, everyone is going to tell you that where the cost comes in is the supporting mods that come with the more cubes. And all that depends on what you are trying to achieve. In my case with the 331, I would want something good for the street and would hopefully be around 350hp n/a at least.
It is a somewhat hard decision though because I have always wanted a s/c, so I have been pondering the idea of a nicely built 306 and throw a s/c on it. Only because the chances of splitting a stock block with the 331 increase significantly with h/c/i and boost. Of course if you can afford it, get a dart block or something and throw the worries out of the window, then you can run a lot more boost. The other thing is, I'm going to be getting h/c/i when I build the short block, so why waste my time with a 306 when the new mods work better on a 331. Plus if the cost difference is 400-600 bucks, the hp gain is worth it. My .02 cents....