I think a lot of people were expecting more of the electro that they pioneered and got turned off by the heavy disco influence.
Electro / disco is not the right dichotomy, as their music has always sat at an intersection between genres. Homework, Discovery, and Human After All are all heavily sample-based, and there are like 1 or 2 samples on all of Random Access Memories. That is the big difference.
Which is (in my opinion) "innovation". An innovation not everyone agreed with.
Instead of sampling from the 70s, they used artists that created music during the 70s.
I think it goes deeper than that. They practically defined the 2010s electro genre, with heavy use of aggressive synthesizers, drum machines, and vocoders for nearly all the vocals. RAM was cleaner, more understated, and very, very slick. You could be forgiven for thinking it was a completely different band. Of course all interpretation of musical genre is subjective. :)
It probably depends on how old you are. When I was rounding out my 20's and still going to clubs, Homework dropped, I listened to it so many times (but looking back, that album was kind of inaccessible to most unless they were already techno-heads). And then 2001 and Discovery, which I'd personally consider their magnum opus, and everything after that is just kinda meh for me except for the TRON remixes (which figures, since I'm an 80's kid).