As far as perception of the album as a whole, my initial perception of the album was fairly low, and that had nothing to do with Portnoy's comments. As I have said, I became a fan in '92 with Images & Words. But my fandom was fairly casual. I loved that album. But snippets and songs that I heard from Awake, ACOS, and FII didn't grab me, so I did not buy those albums until much later. I was in the L.A. area a bit after FII came out, and I think it was Burning My Soul that I heard on the radio. The overall sound of the song was okay, but the lyrics were a bit offputting. So given that I wasn't a big fan outside of Images and Words anyway, I did not initially feel any compulsion to dig deeper into this album.
It was not until late 1999 when I discovered SFAM and bought it on sight that I truly became a big DT fan. That was the point where I then went back and began buying up their back catalog. I got Awake and FII together (I think I ordered them from Amazon). I immediately liked Awake and immediately disliked FII. Part of it was the production and overall sound of the album, which just seemed a bit off to me, part of it was that I didn't like a few of the songs (You Not Me, Burning My Soul, Hollow Years, etc.), and part of it was the number of ballads/slower songs. So, I initially had a fairly low impression of the album just from what I heard. And it wasn't until several years later that I became aware of the backstory and that Portnoy did not like the album very much.
As I became familiar with the songs over time, I grew to really love the album. I can really appreciate most of the songs now. But that said, it still ranks more toward the bottom of the DT discography. That isn't because it isn't good. It is just because most of the other albums are better.