I haven't actually played VLR myself yet - just read readthroughs and the like - but to be honest, I don't see myself actually buying any of it.
When you have time shenaniganery going on, as well as multiple endings, of course things are going to get complex. But I feel like 999 managed to have a tighter story because it wasn't focusing on being a sequel. VLR's story seems to do some meandering, a la Dragon Age 2, and that's not entirely its fault - after all, it has to pick up the story from the first game. That's a tricky make-or-break moment in any trilogy. Either you get something brilliant, or you get something that just seems to tread water while waiting for the third installment to show up and be interesting.
Honestly though, I felt like the setting of what happened in-between made it lose a lot of heft as a scary title. 999 struck a chord because the characters all felt like relatively normal, everyday people. That's why Ace's betrayal was such a punch to the gut. That's why Clover and Snake's relationship felt so true. These are people where you feel like you could walk down a street and pick out their counterparts - well, okay, maybe less with the wacky costumes, but you could certainly tell the same stories. An older brother who is out to look after his sister come hell or high water because they only have each other. A man who seems like a friendly patriarch until he is pushed into revealing his true intentions and motivations. A mother who dresses how she pleases and knows that people are surprised by her talent because she doesn't fit the stereotype. Et cetera, et cetera.
Most importantly, though, was Junpei. A pretty normal dude who gets kidnapped from College. That gets scary because HOLY SHIT I GO TO COLLEGE, I COULD SUFFER THE SAME FATE!
...but in VLR suddenly it's revealed that it's half past the seppuku apocalypse and also you're on the moon. Okay, we're in the future, but that takes away a lot of the sting. Nobody who plays VLR is going to go "HOLY SHIT THEY'RE ON THE MOON JUST LIKE ME!" - they've intentionally put in that distance. That for me is why 999 is scarier than VLR in a nutshell. I think Yahtzee touches on the same in a review for I believe Condemned 2. The first one was scary to him because the final boss was dodging an axe murderer while running through a normal everyday house. The second one ends up with a magic-enhanced fight on the top of a sci-fi tower. One of these things is more immediately relatable as a setting, and one... well, ISN'T.
Right now I've kinda fallen out of love with Zero Escape. I'm hoping that maybe the third game, if it ever happens, will woo me back with chocolates and roses and an understanding that connecting with the player is a good way to make things more immediately emotionally effective. I can hope, I guess.
(And doesn't Danganronpa actually come after 999? I seem to remember at least one 999 shout-out in the Diggitydang Rompus that my friends shrieked about.) (Edit: Yeah, 999 came out in Japan in December 2009, whilst DR came out in November 2010. So I'm guessing 999 didn't rip off DR or if they did morphogenic fields were involved so they deserved it

)