The best tools don't always mean best player!
Often I have said and believe that the feel for the game is just as important as any of the tools. I really think it is a natural ability, just like running, jumping, throwing, etc. Some have it, many don't.
Not sure exactly how to describe it. Maybe it is the ability to make the right decisions without even thinking about it. maybe it is simply instincts.
Whatever it is, Pedroia has lots of feel for the game. The link by Ripken Fan is a great example.
We knew a player, went in the first round, had unbelievable tools. He was a legitimate 5 tool prospect. He did make it to the Big Leagues, but his lack of feel for the game never improved. Released after a couple years.
Even those with great tools need to have this feel to reach their potential. This feel for the game has helped make Pedroia a super star. He has probably come as close to reaching his full potential as most anyone in the game.
Seeing that nearly all ML second basemen were once shortstops I don't think making it as a second baseman is very easy. It is very rare to see a HS second baseman end up being a major league second baseman. So that means you have to be one of the best shortstops to be a next level second baseman. Now we are really getting competitive!