Honestly, having played 999 on ios and VLR on the vita, I'd rather play VLR without the puzzles. Having been stumped in a room for over 90 minutes because there was a shitty darts puzzle that had me pulling my hair isn't exactly my type of fun.
However, if you want to make an argument for how 999 is better on the DS due to how the game takes advantage of the hardware, i'll back you on that. When i read about the key differences between 999 ios and DS, the one thing i wished i had experienced was how the hardware fit into the narrative. that stuff isn't quite as effective on ios, but if the ios version is the only way you can experience 999 then it's still better than nothing.
yup, here comes VLR: the Visual Novel. Might actually be better than the original, tbh.