One of the things about the Superman mythos that always bugged me was the idea that Krypton was supposed to be such an advanced civilization, yet they only had one or two spaceships they could evacuate the planet in, and no one (or almost no one) was offworld when it exploded.
Various explanations have been given for this, usually along the lines of the Kryptonians giving up or getting bored of space travel, but that never made much sense to me.
So how about this: They gave up on manned space travel, because they figured that it was cheaper and easier to explore the universe with robotic probes. So Superman/Supergirl/et. al. will still be the last surviving Kryptonians, but there will be all of these probes and robots out there, you could have stories with Superman investigating them to discover more about his people, or fighting them if they become hostile, etc.
Just an idea I had... I know the DCAU version of Brainiac is sort of like this, but not quite what I have in mind.
I hate to say it, but the crossover idea of Galactus having destroyed Krypton: that gave me da chills.
What I've pondered is how Kryptonians can be so human in appearance, humans can't tell the difference, yet they're that different, that they become godlike under our sun (which does nothing of the sort for us). Sup wit dat?
Possible answer: both come from a common stock, progenitor humanoid race (eg, like the Preservers of ST:TOS), seeding the universe with variations of their original genome. This would actually explain all the humanoid races in the DCverse (just like it did in Trek, according to "The Paradise Syndrome").
Shinier than a speeding bullet.