I do think position scarcity has to be taken into account, but not to the level where we leave production on the board in the third or fourth round. 2B is scarce, but if you take a 2B in the third round you're looking at Brandon Phillips, who went 30/30 last year, or B.J. Upton, who went 24/22 and will likely get more ABs this year to improve those counting stats. Those number warrant a selection in the third round. By the time Victor Martinez's 25 HRs are a good pick, he's he's off the board. Yes, you have to take scarcity into account somewhat, but you can't let it rule your thinking.
Quite honestly, I probably wouldn't take either Phillips or Upton in the third either. But I know wouldn't take one of those catchers till the end of the 4th or beginning of the 5th, and I know both will be gone before that. So I take them out of my gameplan from the start. If I want to be extra prepared (and I have a little free time), I'll probably make a secondary plan just in case one of them makes it to where I feel comfortable picking them.