"I think tools scouting completely worthless on first-year guys anyway...BA can tell me who's got the most projectable power or who's got the best foot speed...but I can figure that out long before they reach the majors ANYWAY just by looking at the stats as they progress"
If that's the case, your idea of the Top 100 prospects is going to omit about 25% of the prospects that belong there. Are you seriously going to tell me the M's, today, value a Greg Halman over a Jameson Taillon?
Most top 100 prospects, especially college players, are not going to spend a significant amount of time in the minors. They're going to spend a very insignificant amount of time at any one level. All minor leaguers have an adjustment period their first month or so at a higher level, so the full data at any one level is not necessarily relevant. Minor league stats are extremely contextualized, really from one team to the next - levels/stadiums can dramaticially influence some players and not others, and the influence is not always significant depending on the specific player. The minor leagues are a time of growth and development; statlines from prior seasons are sometimes not telling at all about a prospect today. Ultimately, you're left with small sample sizes of extremely contextualized data.
Can Nick Franklin catch up to a 95 MPH fastball batting right-handed? What's the likelihood of him staying at SS? How much should we expect him to fill out physically? Will he be a base-stealer in the majors? How's his work ethic? These questions are also important to determining a player's prospect value and cannot be answered by a statline.
BA's scouting is not a bunch of guys gathered around a computer screen watching YouTube videos. I'm not sure if they even aspire to do scouting on their own. All of their scouting reports are coming directly from GM's, coaches, scouts, scouting directors, and player development employees. Their rankings reflect how the prospects are actually valued in MLB circles at the time of the snapshot. A Top 100 prospects list should aspire to do no more (or less) than that, and no one else has been around long enough to build the networks necessary for such an ambition.