I'm far from a baseball prospect expert, but to my understanding the Mets' top end is pretty good with Alvarez who is a borderline top 5 guy and Baty who is top 20. We also just added Kumar Rocker who is going to be right up there.
The Szapucki injury is interesting because he actually already got a cup of coffee in the majors and was maybe a possibility if injuries piled up in the rotation again, but that door has obviously closed now.
Alvarez is a legitimate stud, as is Baty. Vientos is actually a month younger than Baty and mashing in AA. Mauricio is considered a high-end SS by most but is sort of similar to Andres Gimenez in that the production has not yet matched the tools. Pete Crow-Armstrong has potential GG-caliber defense in center and developing hit tool with a lot of upside. Those five position players are legitimately good and would be in any system. They have a couple other interesting guys like Carlos Cortes (who they drafted twice, LOL) and Alex Ramirez.
In terms of arms, that's where it's kind of bleak and helps explain why they used picks on them early. They have Matt Allan who was also a legitimate stud, but is out after undergoing TJ before the season, and JT Ginn who just recently made it back from the same. Beyond those two high-end guys, you basically have Szapucki, a couple guys who are really far off, and then Megill and Diaz who we've already seen this year.
The system has some excellent prospects at the top but is painfully lacking in depth, particularly arms. Adding Rocker is huge to the system, and some of the other arms they took should also really help balance things out.
EDIT: It's not really a reflection of the system's overall strength, but the Mets' farm teams are like historically bad. Syracuse is 19-40, Binghamton is 22-35 (after starting like 0-13 or something), and Brooklyn is 19-39. The best they have is Low-A St. Lucie at 31-29. It's really amazing honestly.