Owned STLE for approx 2 years and a big advocate for that pin - currently own SMVE for nearly 1 1/2 years. Here's my thoughts:
STLE flows way better but shots do feel good on both machines. The warp ramp is simply awesome and one of the best shots in pinball, unfortunately it doesn't have the best rules associated with it. The venom upper ramp is very cool and satisfying to hit as well, but the warp ramp is pure awesomeness as far as fun factor in hitting it consecutively.
Black Suit MB vs Klingon MB. Coincidentally, both these multi balls have nearly the same rules. Klingon mb is better with the light show, lasers and call outs going on; however, BSM is better as you can continue to progress through the game (i.e. villains) as you play.
SMVE wins in art and animations.
STLE wins in call outs and sound effects but I really love SMVE's call outs and sounds too.
So both games play well, both are integrated well. Fun factor for STLE is the warp ramp, fun factor for SMVE is everything else. SMVE destroys STLE in the rules dept. as there's more breadth and progression going on in SMVE. I do give the mini wizard edge to STLE with Kobayashi Maru beating out battle Royale. But again, BR is a fun mini wiz mode. SMVE wins in the wizard mode department; Super Hero is one of the best wizard modes around with a very rewarding bonus for completing - SMVE also has combo multiball. While Combo mb is hard to achieve, super hero is doable unlike 5 year mission on STLE. Both games have similar shot multipliers, but STLE is broken and doesn't award the multiplied shot on a combo - only non combos reward the multiplier shot. SMVE has double and triple shot multipliers that work, so it gains the edge here.
Ball Times: Both games can have long ball times - I removed the center post and put lightning flippers on my SMVE - its a much more satisfying game with this setup as it's more risk/reward building.
All in all; both are great fun pins. STLE is awesome for it's smooth shooting, light show, and warp ramp. SMVE wins in all other departments especially rules; for this I give SMVE the nod over STLE.
And I think Keith Elwin said it best in a recent interview on Slam Tilt; games are best when they have around 5 modes and other stuff to shoot and activate. Games that are linear with 18 modes which are all similar from the next aren't as fun.