The problem with Superman
His home planet explodes leaving him the sole survivor.
Okay, the first problem is planets do not explode on their own. Albeit, they made it sound reasonable (especially after kryptonite was invented and they said the core was now made of a deadly amalgam of nuclear waste), but it's still impossible. To explode the planet would have to overcome all the gavitational forces holding it together. This is a great deal of force to overcome. I'd buy it if the planet was smashed into smithereens by another planet (this can, and does occur - albeit infrequently) but simply blowing the planet up due to what's in the core or something similar is nonsense.
The second problem - he's the only survivor. Again, this makes little logical sense, and makes increasingly less sense the further you go in time. At first he's the only survivor because rocket technology apparently doesn't exist on Krypton - at least not in the stage where it could transport a host of people around. As Krypton becomes more technologically advanced the reasons no one else escaped on rockets becomes increasingly far-fetched ranging from the scientific council refused to build the fleet because they didn't believe Jor-El to the planet's entire population was 'genetically bound' to Krypton to keep them from leaving.
So the whole of the population except one is killed. Except those in the Phantom Zone. And Kara (most of the time). And the entire bottled city of Kandor. And the Daxomites - who apparently left Krypton sometime before its destruction but are otherwise genetically identical to Kryptonians (except they have a weakness to lead instead of kryptonite). Does anyone else see a problem with this?! I mean you make Superman unique by basically killing everyone else off then reintroduce more people from the same planet (or close off-shoots)? What's the point?! Why not have a different origin entirely? Why not something more reasonable?!
And then there's his powers and kryptonite. Okay, Superman's powers and abilities have evolved over time and, let's face it, make him something of a god. They aren't, I suppose, so strange if you consider other superpowers but his means of getting them - Earth's yellow sun - makes him sound like he's part plant. There's also the fact that in order to be livable near a red sun Krypton would likely have to be close enough for the stellar radiation to be similar to that coming from our own. There's also the fact that in the original Superman's abilities were common to native Kryptonians, which actually made more sense.
And kryptonite - ah kryptonite - how your green glow warms my heart. The only thing Superman is vulnerable to (besides magic, which hardly counts). Why? Well it's a deadly radioactive substance - so deadly, in fact that while it can almost instantly kill Superman it has almost no effect on humans whatsoever except over a prolonged period of exposure! Does anyone else see a problem with this?! Or the fact that when Superman's powers leave him he's no longer instantly killed by kryptonite? Or if someone else gains his powers they are suddenly as affected as he is?! Not to mention that it comes in a variety of flavors, all of which have different effects (sometimes very different, depending on who's doing the story) and none of which are as deadly as the green variety.
So, though I know I'll never be in a position to create my own version of Superman, here are two scenarios that I think might be interesting:
1) Superman comes from the continent of Mu. The Muian civilization reached heights we have yet to achieve and developed the ability to alter their genes through a green crystaline material they found while exploring a world through a warp gate. They decided to try and alter themselves to become 'perfect' but were worried this might not work well and so developed twelve babies instead. If all went well the process could be applied to them at large. If it didn't - well at least they'd know. They decided to release only four of the babies into society, since the babies were so powerful, and leave the other eight in stasis. These babies would grow up to be General Dru-Zod, Faora Hu-Ul, Quex-Ul, and Ursa Jax-Ur. Although the four were ultimately defeated once their motives became clear Muian civilization was virtually destroyed. The other eight babies had been sent into orbit, disguised as asteroids, by Jor-El once Dru-Zod's motives became clear - in the hopes they would some day return and overthrow the superpowered dictator. After they were defeated there were no resources left to try and retrieve them and they remained in orbit until, one by one, they eventually fell back to Earth. Eventually those within would emerge as Wonder Woman (Diana), Mr. Majestic, Superwoman, Superman, Supergirl, Superboy, Powergirl, and Powerboy.
2) Superman is the child of Metis and Zeus - the son prophesied to overthrow Zeus long ago. Metis escaped from Zeus one night as he slept. Knowing well of his dalliances, she disguised herself as a mortal woman and lured Zues into having sex with her again. After doing so she used her powers to hide from Zeus and, later, hide her son among mortals. She chose the Kents because of their values, and has since been looking over him and helping him as she can. She is aided in this by Hera who feels no particular qualms about the many battles Clark faces. Supergirl and Superboy would be descended from other deities, most likely Ares or Hephaestus.