I think part of the problem with Big Generator is that it took seven years or something like that. 90125 was huge, with "Owner of a Lonely Heart" and the amazing return of Yes, and people were waiting to see what the follow-up would be. They kept waiting, and waiting, then when it finally arrived, it seemed like literally just more of the same. That's how it was for me anyway, and I know others who feel the same way.
However... your points are all correct. Big Generator, despite having a similar "sound" to 90125, actually takes things a bit further, quite a bit further sometimes, just not in the direction people were expecting. Old-school Yesfans dissed 90125 for being Pop. Damned good Pop, but still Pop. Big Generator is actually proggier and takes a few chances.
The biggest problem, therefore, is that it falls into a very narrow niche. It still wasn't proggy enough for old-school Yesfans, and after seven years, the "new" Yesfans who came on board with 90125 had given up already. It is only now with the benefit of perspective that we can appreciate the album properly.