Yup, they really stepped up up the puzzles thought, 16 unique and fleshed out puzzle rooms vs. 9 clunky ones. But ultimately VLR doesn't feel as complete as 999 did for me. It left me with more questions and fewer convincing answers. There were promising elements that never really developed (the whole Ally/Betray angle was an undercooked plot device, for instance). And overall the game lacked the thrill, urgency, and gruesomeness of 999... it felt cleaner, more sterile, mostly because of the 3D visuals and art-style.
In the end I thought it was a great package, with better gamey parts and worse narrative than 999. I'd place 999 on top because it felt more satisfying, especially when the true endings are compared*.
* According to an interview with Uchikoshi, the incinerator puzzle and twist was *the* first thing he came up with for 999, then developed the whole game around it. He's in love with it. And it showed.