Yes, I did see mention somewhere (if I'm not imagining it) that the Matrix and Vector classes were on their way to deprecation, so I've just been avoiding them.
Part of me does kind of feel iffy about a library becoming less and less diverse, but when I really sit down and think on it, it is just a parallel of OpenGL itself, which has been removing crap with every release and just letting the programmer do what they want.
GL has improved vastly since 3 came out, in my opinion, because people are being forced to really think about what they do instead of just pushing and popping everywhere. I admit: I had horrible nests of that myself, and now that I'm having to actually manage my own matrices and upload them to my own shaders, I've collapsed my entire system of matrix usage to a bare three tiers and a lot of caching, and overall it feels awesome.
So, once my knee-jerk reaction is over, I'd just like to say I agree.
Also, I had no idea you made Revenge Of The Titans (just noticed your signature), and I must say, though I don't like that genre of game, I do really like that game specifically, from seeing TB's video on it. If you made that using LWJGL, I feel confident I've made the right choice of library for my own project.