I really hope that DC will find a good way to bring back the Elseworld stories. I don't know if it should be an anthology like "DC Universe Presents" or some one shots within the regular releases, but I love these alternate stories. Something like the Batman of Shanghai was awesome, or a story with these greaser/rockabilly Batman characters would be great.
I'd imagine, though, that any Elseworld stuff would end up being digital first, which might be okay. Either way, seeing more Thomas/Martha stuff or Batman in other time periods/personas would be fun.
I doubt they'd ever return to that universe, but it sure was an interesting place, one that I would love to see more of as well, and yes, Thomas Wayne as Batman was badass. He might not have had all of Bruce's tech, but hell, he didn't need it! There's so much potential there, in the "Flashpoint-verse", that it's a shame it'll probably never be properly exploited.