Well... first, to get it out of the way, I'd say that there's absolutely no chance that its type will change. None at all.
That said, Gyarados obviously IS a dragon. That's why it learns Dragon Dance and why it's in the Dragon egg group. I would have to assume that it was meant to be a dragon all along, but simply wasn't made Water/Dragon in Gen I because there's nothing that could've countered it. It was (and sometimes still is) hard enough to counter it as Water/Flying - as Water/Dragon, it would've been plain unstoppable. After five generations of new pokemon, it'd be possible to counter it now if it was Water/Dragon, but still potentially damned tough - that's just a particularly strong combination, and Gyarados is a particularly bulky AND hard-hitting pokemon. But it could probably be done. But it won't. It's a pokemon and it's Water/Flying and that's just the way it is.
I would like to see it get a physical Flying move other than Bounce though. It can't even get a decent HP any more, since HP is special now (I've got an Adamant Gyarados with HP Flying in Ruby and it's terrifying).