Really interesting question.. Totally agree with SantaEatsCheese that ST:TNG has to be included for ruleset and assets alone. A few more that came to mind based on layouts, rules, and the "feel" of a newer Stern:

Stern Cheetah
Three flippers, lots of tight lanes, drops with progressive awards, under-the-upper-flipper shot.. feels proto-Elwin in some ways

Sega The X Files
Lots of bad examples of this game out there, but when it's shooting smooth X-Files has some of my favorite shots in pinball. Both ramps are fairly challenging and the game plays FAST even if the code isn't the deepest. Watching Robert Gagno light it up is always a treat.

Williams Demolition Man
Code and layout that pushes the player to shoot quickly, know the rules, and execute. Played this game a lot on location at No Quarter and it grew on me more than I expected.

Gottlieb Victory
Four flippers, super cool upper playfield with multiple ways to get there, and rules that lend themselves well to the theme. When Victory is playing fast it FLOWS. Lack of multiball is kind of a bummer, but I dig the music and there's just something about trying to hit each checkpoint that keeps bringing me back.

None of those games are EMs, but I can understand separating early-SS and DMD-era games if that's what you're getting at.