Finished 999 today, which I've had in my backlog for years. I could see most of the plot twists coming from a mile away, but I thoroughly enjoyed myself and the remastered version was a really smooth experience overall. (I've heard that the original DS version was a bit of a pain due to lack of a flowchart and whatnot, so I guess you could say I got something out of waiting until now to play it.)
In comparison, Virtue's Last Reward, which I've now started, seems to not have aged quite as well. The gameplay feels more sluggish, the text speed is horrendously slow, and the 3D models make the characters seem much less alive than the 2D ones in 999 did. It also feels pretty weird to have a silent protagonist all of a sudden, and it definitely isn't doing him any favors in terms of making an impression on me. That said, I'm still just at the beginning, and I expect the story to be quite a ride, with a lot of character development.