Derek Carty has an article he posted at The Hardball Times that elaborates on a system he uses to track hitters "true" power numbers by measuring fly ball distances and adjusting for weather and atmospheric conditions. Carty finds that by doing so, it is easier to determine what a hitter's home run totals should bu from year to year, and it becomes possible to explain why some highly regarded sluggers experience significant drop-offs in their home run totals on occasion.
I like the idea of Carty's system, and I think as more information becomes available from computerized monitoring programs used at MLB games we'll see a lot more applications like the the "True Home Run" Tracker. I would like to see a system that utilizes ball speed off of the bat, spin, and initial trajectory angles since home runs and fly balls are part horizontal vector and part vertical vector. There may be some hitters that create better spin and traject hit balls at more favorable angles with higher speed, and those types of stats could help create a baseline of data for analyzing which hitters have more true power regardless of weather and atmospheric conditions.
As for minor league players, we might have to wait a while for such systems and consequent data to be available to the public. There is a significant initial investment in the software and equipment needed to perform accurate and detailed in-game measurements, but I wouldn't be surprised if some teams already have them in place at some of their minor league parks and we just don't know about it. Either way, there are some very interesting things going on in baseball right now, and it's quickly changing the way the game is tracked and understood. I guess some purist might think that such changes are subtracting from the game, but I think it will only add to the overall appeal and entertainment value of baseball as a whole.