You know, I have to say, the intelligent debate between these two is sorely missed. While I often disagreed with Siskel, his reactions and critiques tended to be a lot more rational than Ebert's, who often has much more of a gut reaction for better or worse. And don't get me wrong, I'm a huge fan of Ebert, especially his writing, but it was the dynamic between these two that made their partnership so great.
As for the critiques itself, I think Ebert's points were mostly valid. The color footage isn't very exciting, especially as it's the same thing for the whole last movement of the film, and he's also not the first to point out the lack of audience shots. And while it's funny to see the band laugh when asked what the point of the film was, because we know them so well and like to see them more relaxed and fun, it does come off as childish to non-fans, who are probably going into the film wondering what all the hype is about.
I liked how Siskel turned Ebert's comment about B.B. King around, and I also find it to be one of the least successful parts of the film. King's praising of Bono's lyrics says less about Bono's skills (esp. at that stage in his career) than the material that King ususally has to work with--When Love Comes to Town ain't exactly Dylan.
They also both have intelligent points about the gospel church scenes. This time it's Siskel who has the emotional reaction, while Ebert probes a bit further and wonders why we're not given a better look at the people who U2 are performing with.
We all know R&H isn't a perfect film, it's that we enjoy seeing these glimpses of the band behind the scenes and the great performances. But I think you would have a hard time arguing that it's on the level of Don't Look Back, The Last Waltz, Gimme Shelter, etc.
I'm curious though what Ebert's review of U2-3D will be like, because he's definitely receptive to breakthrough visuals in moviemaking.