It might mostly be because I'm happy to see real Jon again but I have no problem with Super Sons being the focal point of Damian's story here. Nor have I ever felt that their friendship was only beneficial to Jon and a hindrance to Damian as a character (if we're being completely honest, that's more how I go back and forth on feeling about both of his Titans teams). It damn sure didn't set him back in any way. If anything, I feel it's a testament to how far he's come
With Colin gone from existence, Damian finding another kid his age (or...close enough) and forming the kind of connection those two had is one of the best things to happen to him while he was on the road to being a better hero and a better person in general. He needed someone like that. A friend he had that was outside the family who could be a foil to him but also share a deep connection with. Granted, that person was Maya first but Tomasi and Gleason seem to be the only ones who thinks she's marketable. Not that it matters, anyway. People are allowed to have more than one best friend.
I've always thought both Damian and Jon brought out something in each other that they couldn't get from their other friends and family.
For Jon, being with Damian showed him the life of a hero outside of Superman's world. When they're together there's this stronger sense of Independence that I get from him that you didnt see as often in his Dad's titles. Despite being written by the same person, Jon felt different in Super Sons than he did in Superman. And whether that was intentional or now, I always felt it was a really nice touch.
For Damian, Jon brought some MUCH needed levity. Especially with him going through all the bullshit he's still enduring in other titles. His time with Jon was the time he had to unwind, to have fun, to forget about the not so great stuff that was happening in his life around the same time. For once in his life, he had someone close to his age that he could let his guard down with, even if it was just a little. Someone to be protective of. Someone he got to try just being a kid around. Some may disagree but I enjoyed seeing that side of Damian. I thought the softer side Jon brought out in him could have been beneficial to him as a hero had their friendship been allowed to continue the way it was.
NOW however, with Bendis at the helm and Jon now a whole seven years older, I feel like their dynamic actually has become what detractors were saying that it's been from the start. Damian looking bad for the sake of making Jon look good. They don't feel like equals anymore. Now it's like...the mature, experienced big brother and the bratty little brother who doesn't know what he's doing. Which not only completely wrecks the kind of relationship they had before but is already VERY similar to the one Damian already has with Dick.