I heard FII for the first time in late 2001/early 2002. Didn't like it at first, but came to like it a lot over a period of about a year. I had no idea what Mike Portnoy's opinion of the album was at the time, so it had no influence on me whatsoever. I had heart Burning My Soul on the radio when FII came out, and didn't like it, so I never bothered to pick up the album. After hearing a couple of tracks from it on LSFNY, I picked it up. I was immediately struck by how different it sounded, and didn't care for it. But like I said, it grew on me. I don't think it's underrated at all. It's a very good album, and I a lot of fans recognize it as such. As far as individual tracks:
-New Millenium: I didn't know it existed until after I had heard Caught In A New Millenium on LSFNY. I like the Caught version better, but the album version is still a terrific song. Liked it from day 1.
-You Not Me: I've never liked it. Still don't. You Or Me is slightly better, but I don't like that version either.
-Peruvian Skies: Kind of a slow grower. At first, I didn't love it; didn't hate it. Now, I really like it. Would love to see it live again.
-Hollow Years: I have never liked this song one bit. The extended versions they started playing from the TOT tour onward take it up a notch or two, but even then, I don't like it.
-Burning My Soul: Didn't like it at first. Now, it's okay. It has some really cool parts and some parts I don't care for. But I think it would be a great live tune, and I'm hoping they bring it out sometime.
-Hell's Kitchen: It serves as an okay warm up intro to Lines In The Sand. As a whole, I don't like it one bit. Definitely my least favorite instrumental by DT (although Eve gives it a run for its money).
-Lines In The Sand: Best song on the album.
-Take Away My Pain: Demo version is better, but this is still a great song.
-Just Let Me Breathe: Not great, but very good.
-Anna Lee: Very nice ballad. This song is easy to overlook given the other ballads on the album, but very solid.
-Trial of Tears: Took me a little while to warm up to completely, but I love it. Second best song, closely behind LITS.
The other songs that didn't make the cut, which I didn't hear until years later, are hit and miss. Some very good ones and some that are decent.