FII is awesome, and I always had the impression that a lot of the fanbase's resentment stemmed from the band bad-mouthing it.
rumborak
Possibly, but I also think it's become more "acceptable" as it's become less contemporary.
When you've only got Images and Words and Awake, FII is immediately dangerous and must be stopped at any length. But the more albums that succeed it, FII becomes less of a danger or a hint at a shake, and more of a quirky footnote.
Not to mention, as Dream Theater get older, they alienate the older fans - as any good band rightly should; if nobody's got an opinion then you're not doing the "career" thing right - and the newer ones fill their places. The people who remember being scared by FII will have been gradually shed, whereas if they've joined, say, post SDOIT and further, it won't have as much historical significance for them, and it's easier to judge on its own merits.
The albums seem to all undergo reappraisal. There are some who liked them when they first came out. Some who've always hated them. But the new fans will always tend to be more sympathetic to the entire, collected back-catalogue, 'cause they don't have to worry about a direction that the band might have wobbled towards ten years ago, and if they weren't constantly finding material that they enjoyed they wouldn't be joining the good ship Dream Theater in the first place.
Wasn't too long ago that SDOIT was the scrappy of the catalogue. Only 8 years down the line has it really buried itself into the collective consciousness. Partially 'cause the ones who didn't like Six Degrees when it came out have long since given up, partially 'cause it's nothing to worry about any more. Train of Thought is starting to get the hate alleviated, too. Only slightly, but the fan-base is slowly pivoting around, like a massive boat changing direction. That's grand. I've always liked Train of Thought.
NB: This was possibly a tad repetitious. I am drunk. Hello.