ReaPsTA pretty much nailed it, but I want to address the three main points in the OP:
1) Not enough masterpieces. I mean, you have AMBI, which is fantastic, and SD-V (I'll probably lose some credibility at this point), and the first half of Scarred. But then you've got CIAW, IF, Lie, 6:00, and The Mirror, which are definitely fun songs in the right context, but in no way compare to most of DT's material.
If we can assume for the sake of argument that those songs you mentioned are the least best songs from
Awake, those songs take up about 40% of the album. I would then submit that no other DT album, except for maybe I&W, has that strong of a bottom 40%.
2) Poor production. Examples: poor editing at 7:11 with LaBrie's "-TAAAAAAY", early cutoff of the end of SD-V.
Not sure what JLB part you are talking about (at 7:11...huh?), but the production and sound of this album is arguably their best, surpassed only by FII, possibly. But it sounds terrific. Okay, if you are only listening on computer speakers or mp3s, then maybe you'll have a tough time hearing it, but if you listen to the actual CD on a good stereo, it sounds terrific. It is dark, moody and airy. To make a comparison,
Train of Thought also sounds dark, moody and airy, but that record is compressed way too much (I always say how the beginning of "This Dying Soul" sounds like you are listening to the song with blankets over your speakers), while
Awake has tons of room to breathe and thus sounds very alive and fresh, even to this day.
3) Lack of variety. You have two types of songs, without much of a spectrum in between--the heavy riffy side of Lie, and the ballady side of LSOAD. Compare with an album like FII, where you have a huge variety of sounds.
Two types of songs? That makes little sense, unless your views of "types of songs" is extremely broad. Since I would assume that you would say "The Silent Man" and "Space Dye Vest" fall under the same ballady side, are you going to tell me that they sound similar?