Update

This system is usually the opposite: a couple of blue chippers, precipitous drop-off. There’s not much on the top end here now, but it could be a very different story next year if some of these intriguing players pan out.

I agree it´s a very tough system to get a good grasp on.
It thoroughly lacks players who were high-profile guys prior to the June drafts – with the exception of Matt Harvey. Instead it probably features more International prospects than any other system.
It has some players with very nice tools who were promoted aggressively at a young age and thus have posted mediocre stats.
And it has some players who have posted very good stats but either seem limited tool wise or were actually a bit old for the league.

I wonder how much the perception “Mets are a dumb organization” will play a role in the grades.

I think the Mets system this year has had as many bats with age appropriate numbers as any system out there. If I do a purely statistical analysis, using data from baseball-reference, using runs created per game (using OBP x SLG x 33.5), park and league adjusted (easy enough since I’m using “runs”), the Mets end up near the top in what I consider guys with age appropriate numbers.

The thing is there aren’t a lot of future stars there, it’s more guys who look like they have a chance to be solid regulars. But there is more depth then there has been there for awhile. The Mets seem to have been emphasizing the hit tool, and drafting and signing a lot of guys with enough tools for positions like 3B and RF. Especially in their international program, they aren’t signing the toolsiest star potential guys, but seem to be finding guys with solid tools and some hitting ability.

The pitching is where you can really get bogged down with all the grade C guys though. Lots of guys with either big arms and poor numbers with questionable command or feel for secondary stuff, or good command and and feel, and good numbers, but with very average stuff at lower levels that you aren’t sure how it will play as they move up.

I actually found the first 35 guys not too hard to rank, but there’s probably more than 15 guys you could consider for the last 5 spots if you are going to 40. Guys like Rafael Fernandez, Yohan Almonte, Mike Hebert, Domingo Tapia, and Nelfi Zapata are guys who could be interesting, but might not make the cut.