Cabinet quality is definitely not what it used to be: https://pinside.com/pinball/forum/topic/sterns-new-cabinets
Decals peeling has apparently been a new trend over the past few years as well (Stern apparently acknowledges that problem and will send replacement decals):
Playfields are commonly exhibiting ghosting and clearcoat issues.
Node board failures with no schematics available for techs to fix them (on surface-mount soldered tiny components, to boot) is another one. Node boards also are not all compatible with one another. To me, that means the games may only last so far into the future before they're obsolete (due to lack of game-specific replacement boards if Stern should fold or abandon support for older titles).
Incomplete code upon release is standard now, and code updates are not on any regular time table either. However, Stern did make a public announcement recently regarding the state of their code, so maybe they are going to make some improvements there.
I will not pretend that JJP is immune to any of the problems Stern or any modern pinball manufacturer is up against, but it appears they are using a higher grade of materials and construction for their games than Stern--and i believe the higher cost is justified for those reasons...not to mention regular code updates and 1.0 code included from day 1. (They're up to version 6.5 at this point, afaik). They're making deep games with lots of toys, multicolor LEDs, ramps, video display, and all the other stuff everybody wants out of a modern game. As you pointed out, JJP's base games cost a couple grand more than Stern's base model... but incomplete code, peeling decals, proprietary boards, and ghosting/crap clearcoat are justifications why they aren't worth as much as JJP games anyway, in my opinion.
I don't really even have a horse in this race, as my first NIB is gonna be from Spooky (TNA, to be specific).