I have my own speculation on the matter.
I think NLOTH revealed that the creative relationship with them is pretty much toast. The best material was the stuff left pretty much alone (and written with E/L) like MOS and the worst material is the stuff U2 kept tinkering with late and were said to have finished last (Boots, SUC, CT) and don't have E/L writing credits.
From all reports it seems they ended up moving away from some of the original ideas. And they have a completed work (at least according to Bono) that was said to be more...downbeat or less straightforward and that has still never seen the light of day.
I sense E/L felt a little burned, especially from some of Lanois' words afterward. Considering they let them write with them and be credited, only to sandwich three crap songs in the middle of that album...this, after scaling back whatever they scaled back. Lanois was hyping the hell out of that record before he kind of got quiet about it all, even after the fact.
It's no great wonder to me, that the 4 songs that E/L did not get writing credits on were the three usual suspects and the dad-rock waltz of Breathe.
I just feel like, in the end, whatever authority E/L had over them, U2 had firmly seized it back by the time NLOTH was completed. And whatever among the interesting musical ideas they came up with, a lot of that was pushed back in favor or Will.I.Am tripe like Crazy and Boots and the dreadful SUC.
In short, NLOTH seemed like the album some of us had been waiting for - for a dozen years, and it just wasn't allowed to come to fruition. Personally, I still believe it's their best album since POP but man, 'what could have been'. That's how I read Lanois comments after the fact. He seemed disappointed.
Maybe I'm reading too much into it but I don't believe so. I feel like E/L probably feel they've done as much as they can with U2. Especially if U2 doesn't trust them as much as they used to. After all, U2 made some questionable decisions for that album, seemingly, on their own.
I'm most curious if they let Burton actually write with them. And if so, how much of that they moved away from in the end.