What they should have done was just NOT reboot at all. The DCU should have just continued as it was before Flashpoint. Hell, Flashpoint wasn't even intended to BE a reboot. Didio, in his infinite "wisdom," hijacked Johns's story last minute. The only thing they needed to do was restructure their editorial management and attract more top-tier talent and also try to get back some of the talent that they had lost like Mark Waid.
If they had to do some sort of "reboot" for new fans to jump on, they should have taken the same approach Marvel did with the Ultimates and launched the New 52 as an alternate Earth separate from the main DC Universe. The Pre-Flashpoint should have remained the main DCU with the New 52 as an alternative Earth.