I also very much enjoyed the way the change wrote the character forward rather than hand-waving away his past, effectively saying, "Those stories don't count! That person's work was no good! Here, mine's better!" The "old" Brainiac was still a part of Superman's history, to be revisited whenever the company liked. Nothing was undone, and something creative was added. 

Brainiac's new mission of battling a universal-scale "Master Programmer" only he seemed capable of perceiving was interesting as well. He saw Superman as an Angel of Darkness and puppet of this malevolent entity. A delusional robot with deicidal tendencies was an interesting direction to go with the character, and an interesting way of redeeming Brainiac as a villain after DC had reprogrammed him into a bland, space-faring good guy.

Since change is always going to occur regardless, and standing in place is unfortunately never a valid option, I'd prefer the changes yield the sort of imaginative results they did here. Had the creators wished, they could easily have taken the new Brainiac apart at some time and reconstructed the "original".* This "Master Programmer" Brainiac sought to displace could have built a new version of his old self from the information it gained in taking him apart in the first place, and set the two in conflict against one another. By keeping the original in the story, the new version was immediately more interesting and credible than he would have been had his history all been made "neverwas."

The New Brainiac was a fun concept with a wonderful visual. I, too, find it regrettable that he lasted such a short time, post- reboot robot stooge call-outs notwithstanding...

I've clearly enough of a soft spot for the redesign to have bought one of the action figures a few years back - seen here with the original, and a similarly-minded friend .....