Huh, I think the opposite. I'd like them in a real relationship. Despite the new 52 showing it is the interconnectedness of character relationships that best illustrate character growth.
Oddly enough I remember reading the reactions to that pairing when I first bought that book, and it was of the few times that I looked and was like "Damn there is real racism at play here and with these resposne". While I almost NEVER blame racism for character choices, it was just too outrageous and overt. I was surprised because I didn't think the fanbase would care about an advancing narrative.
It cemented that they belong together.
Narratively however, where I normally choose to look for answers and it a perfect pairing, its the worlds finest thing.
Supes/Bats
Apollo/Midnigter
Powergirl/Mr.Terrific
Sit back and let that sink in for a sec... its actually a beautiful pairing and... it makes me wonder a few things and I'd personally write that story because its worth telling buuuuuut....
1. Who would the 3rd member of that trinity would be, obviously someone magic.
2. A are there any other half kryptonions visiting from the future, like their kids would be in an arc. Kinda like Franklin Richards
That being said... she can be in the book and NOT be a mainstay, because she should be off having her own adventures. but its a great card to play "occasionally" Also I remember worlds finest huntress/powergirl it was like "man of her dreams" or "a new nightmare" and some reaper looking guy was masquerading as MR.T, but... All in all the terrifics....
A better solution is for them to have LOTS of guest stars as they deal and delve into different areas of science. Time/Space/Reality/Magic etc.