An official Imagineering book isn't going to come out and say "yeah we realize this doesn't exactly fit into Tomorrowland, but marketing wanted it, so..." It's an official book. My opinion, and there is quite a bit of evidence supporting said opinion that's already been outlined, is that the ride is based around the show along with the fact that they are all toys. The former works, the latter doesn't. Remove the latter, the attraction works in Tomorrowland.
That said - the ride is weak. With newer, superior attractions like Midway Mania and Men in Black, so much more can be done with the space. Remember - lines do not exactly equal popularity. The fact that an omnimover has Fastpass is why the lines are so long... it creates unnecessary bottlenecks. I bet if they removed Fastpass the line would rarely exceed 30 minutes.
Wall*E CAN become an excellent dark ride if they use their imagination - keep the ride track intact and transform the vehicles into the People Mover system seen in the movie. Tour the Axiom, emphasize the environmental concerns, reference Buy*N*Large, return to Earth... bam, thematically appropriate, well-done dark ride.