I've always liked FII a lot. Even though I knew it wasn't as great as I&W or Awake when it first came out, I still liked it a lot.
To me, the glaring problem with it is the beginning. You Not Me is obviously not good, and while I like New Millennium, it just isn't a good Track 1. If you look at every other DT studio album, Track 1 sounds like it was written to be a kick ass opening track (regardless of quality). Sadly, none of the songs from the FII sessions have that "kick ass Track 1" feel to it, so it almost feels like New Millennium was placed at the start almost by default, like, "Well, nothing else works as the first song, so we'll go with that." The flow from tracks 3-11, however, is pretty darn great, and even the lesser songs in there - Burning My Soul and Just Let Me Breathe - are enjoyable to some extent when listening to the album as a whole. I know would say, "Just lop off the first two songs and make Raise the Knife the first song," but even that wouldn't work, as Raise the Knife doesn't have that Track 1 feel either.