The way they rebooted Superman and Batman weren't the problems. Both had stories set in the past (the Man of Steel six-issue series and the "Batman: Year One" arc in his title) to re-establish the new versions. But Wonder Woman having her new story set in the (then) present day wiped out all of her past involvements with the rest of the DC universe, including erasing her as a founding member of the Justice League of America. (They then repeated that mistake a few years later with Hawkworld taking place in the (then) present day.)