I wanna go back and clarify what I was talking about vis-a-vis arm length since Dipre's response made it clear that I didn't communicate it well.
First of all, I'm not disparaging Pedroia in the slightest. Dude works about as hard as it's possible to work. That said, the limitations of the body apply no matter how hard you work. He probably developed his arm about as far as he possibly could to try to stick at SS, but without longer arms there's a certain leverage you just don't have no matter how good your technique is.
As a SS Pedroia could probably make every play at shortstop that, say, Derek Jeter, another shortstop with an unspectacular arm, could make. He won't make the really tough plays Jeter never made. The twofold issue with Pedroia at SS is lack of leverage to really muscle up on a throw, and the resulting fact that he'd have to max-effort every throw from the hole. These factors combine to make SS not only a performance issue for Pedey, but also possibly a health one. He's at 2B not because he couldn't play SS if he had to but because what he has to do to make up for that lack of leverage and get good pop on a throw from the hole would put a little extra stress on his ligaments that isn't a factor at second.
With Lowrie, this is less of an issue, because he isn't the pint-sized powerhouse Pedroia is. His body is of pretty much normal proportions for an athlete, and his arm is not only better than Pedroia's, but capable of improving to a higher level without heightened risk of injury, if he's prepared to develop his technique. He's never exactly going to have the arm of an Alex Gonzalez, but he has the ability to show an average or better shortstop arm without messing up his shoulder in the process, unlike Pedroia, which is one of the reasons why Pedroia was very quickly shifted to second and the Sox are looking at Lowrie very seriously as a potential shortstop. One of a number of reasons, of course, but certainly one.
If you have to move Lowrie to second down the line he's certainly proven he's comfortable there, but that doesn't mean you rule him out at short, since he's proven over time that he's comfortable there too. It's no secret that I like the kid, and his versatility and willingness to play multiple roles on the team is a big part of the reason why.