PhrostByte, I agree with what you're saying. I don't think most people see it. It's like Scott Weiland (sp) from STP, once he sobbered up, his music was not as great as the first 2 albums. It's happens with many rock musicians.
Now, I don't know what's going on in Trent's personal life, when he cleaned up, etc. All I know is that these two albums after the Fragile have a totally different tone from his previous works. I just attributed it to him getting older and that usually happens to musicians as they age. To anyone who gets older really, you just don't have the same anger like you did when you were younger (well most don't).
I've listened the Year Zero about 3-4 times over the past two days while at work. While it's better than with teeth it's still not among his best. I'm still trying to capture all the lyrics as I usually listen to the melody first. In both lyrics and in melody he's borrowing a little from his past work and it's noticable. Also his singing ability has changed as well, again, could be due to age.
While his work is still better than most out there, I don't think fans can honestly say this and With Teeth are his top two albums. Go back and listen to everything again.