"It's not you, it's me" is a clichéd phrase when breaking up with someone [0]. It's often not genuine, and even when it is, it's still a degrading situation for the receiving party. "It's not you, it's us" can be taken as a quip on that. It's unnecessarily cute at best.
[0] https://en.wikipedia.org/wiki/It%27s_not_you,_it%27s_me is still unnecessarily cute, and since "it's not you, it's me" is a common p