Marc Bernardin (who among his other accomplishments was an io9 guest blogger) has written his idea of how a Gotham TV show should start and it's fantastic.
Here's what I WOULDN'T do in the pilot: Kill Thomas and Martha Wayne.
Instead, open with the Waynes sneaking out of a charity event, confronted by punks with malfeasance on their minds. Then the Waynes are SAVED by young Lt. Gordon.
This way Gordon and the audience gets to know Bruce's parents. And the audience know there's a sword hanging over the heads of Thomas Wayne and his wife.
THEN, either halfway through or at the end of the first season, you have the Waynes at a similar event — make it a charity screening of Zorro — sneaking out the back, and getting gunned down. Without Gordon there to save them.
That way, the Gordon who drapes his jacket over a heartbroken boy isn't a stranger being nice to an orphan, he's a distraught man also grieving the loss of dear friends. Of good people in a bad world.
This sets up a lot of conflicts. Does the boy Bruce blame Gordon for not saving his parents? Do Gordon and Alfred bump heads as competing surrogate father figures?
But I think it's already been stated that the show starts after the death of Bruce's parents so this isn't happening.
But Bernardin's idea is still worth reading here.