What the Beatles had that is missing today is the songwriting. They brought chord progressions and harmonies into rock that hadn't been used before, so there was innovation there too. They had the attitude on top of that. Criticizing their musicianship reads as missing the point to me. So what if they couldn't play Brazilian rhythms.
One place where Jones didn't give The Beatles their due, was in not acknowledging they were great composers. Jones himself said that the song is "everything". He says that if the song is great, you can get a mediocre singer and it will go over, but that if you have a bad song, even a great singer can't put it over. The Beatles wrote so many great songs as we all know.
Jones is outspoken throughout the interview and is shooting from the hip. He is not wrong about The Beatles as instrumentalists, but The Beatles weren't about being virtuosos, and as I said earlier, I think they would be the first to admit that. I think Jones' statements about them register with most readers as being unfair, and as
@poppachubby says, missing the point about them.
I read on one musician's Facebook page a long time ago, where some of the great jazz drummers who worked for Ludwig, weren't happy about Ludwig making a big deal out of Ringo Starr, and pushing him. Apparently, some of them were assembled one time at Ludwig's offices or wherever when Ringo was there, and they asked him to play something. I'm going by memory here, and either Ringo politely refused, or couldn't play it, I don't know. If this happened, I can understand their frustration and their feeling betrayed by a business they had helped build up, but Ringo wasn't trying to fence with them, nor say that he was a better drummer than them. That feeling of unfairness I got when I read what Jones said about The Beatles, was basically the same one I got when I read about the drummers and Ringo.
I guess it was Jones' remarks on The Beatles that left me initially with a bad feeling. But the guy's a human being, and was calling it the way he saw it. Ultimately I agree with
@damacman, who said the interview was an "enjoyable read, unfiltered, and raw." And as I said before, I agreed with much of it.