Worth considering with Bogaerts is that his BABIP is pretty awful, especially considering the sort of power he has shown. In 238 AB, he has 15 HR, and 64 K. So, he has put a ball in play 159 times and gotten 44 hits. That's a .277 BABIP. While low, that does't look too awful. But, a player with his power should typically have an above average BABIP based on harder contact. I wish there were more first hand reports on his play so we knew if he has had bad luck, pops out a lot, or if its something else. Given the rest of his performance and the fact that his DSL BABIP was .362 (I know, DSL stats, but it's something to go on) I am inclined to believe that his BABIP is flukey.
I think there's a handful of guys that could be considered number 1 in the system, and just to be different, I"ll pick Bogaerts. His .830 OPS and 14 dingers at 18 years old in a little more than half a season of middle A is one of the most impressive seasons I've seen for any Sox minor league in recent years. I like to compare him with Hanley except that for power, Bogaerts far exceeds Hanley at similar years of development. I also hope Bogaerts sticks at short but the high number of errors (25 errors)is a bit of a concern - and another similarity to Hanley!
If he's really a .320 or .330 BABIP hitter with bad luck, we are looking at a roughly .300/.370/.570 line and an OPS well over .900. Mike Stanton is another name that comes to mind as a potential comp. Bogaerts has less power and fewer K's than Stanton, but the BB:K is similar and there are so few players with power at this level at this age that it's hard to find a really good power fit. Guys like ARod and Harper are not great comps as both struck out significantly less at the same age and level and reached the upper minors while still 18. Hanley doesn't strike me as a particularly good offensive comp (defense could be another story) as he only comes close to the power Bogaerts is showing now in his peak MLB years and has no stretch in the minors that looks at all similar to what Bogaerts is doing right now. Also, Hanley's developmental path was pretty anomalous and does not lend itself to comparisons with other players.
All that is to say, ranking Bogaerts number 1 in the system is not something I would object to. I don't have him that high, but I expect him to be there in a year. Actually, I expect him to be a top 10 prospect in all of baseball in a year's time. But, I don't think he's there yet and half a season in low-A isn't enough for me to bump him above some of the very good upper level prospects in the system.