Agree. I have not liked Dream Theater nearly as much once DS was canned, and JR was hired.
Try not to think of it like this. Rudess was who they wanted from the get-go but wasn't available so they went with Sherinian. So when Rudess then became available Sherinian was bumped. I do remember hearing LTE and also the one-time live show they did with Rudess thinking how awesome it would be to have Rudess in the band and then like a month later it happened... and this was before I knew too much of the post-Moore keyboard adventures.
As for rankings, I really don't participate in them, I find it shallow to rank art vs art, particularly within the same artist, I have no problem saying what I personally prefer, but that can also change depending on where my head is at, but I mostly "rank" them all equal cuz they represent a time in my life and theirs that means something for that period.
I also think this conversation would be different had FII been the double album w/ACoS (and/or demo versions) they wanted initially.
My only gripe with FII is the Chapman stick. Unless it's your main thing (Tony Levin), it's just stupid. It was a gimmick they tried when they were trying absolutely everything (which I mostly enjoyed this diversity and experimentation) to please the suits and Myung plays it like a regular bass for most of the song anyway.