With the filming of the new Doctor Who series in the UK, there's been talk of a regeneration story. I have to agree with the idea it would be silly to have a regen story (I'm going to abbreviate this to save typing :P) at the start of the series, due to the fact that after a regeneration the Doctor almost always starts out with an unstable personality and it'd be better to start out with an established Doctor so the audience have a better idea what to expect.
OTOH, I'm all for them doing a flashback to a regen story later in the series. Of course, it's unlikely to be like any regen story we've had before.
Most regen stories are along the lines of "The Doctor regenerates at the start and then has this unrelated adventure". I would think that a modern regen story would make the regeneration part of the story. Little really has been done with the concept of regeneration during Doctor Who's run, other than to use it as a plot device to change the leading actor occasionally.
You could have a story, for instance, where the bad guy tortures the previous Doctor to death, followed by regeneration, then the Eccleston Doctor kicks the bad guy's arse and steals his leather jacket. Or my favourite concept, where the previous Doctor and Eccleston Doctor meet up at the start of the adventure, and at the end the previous Doctor is wounded and sent back in time to the start of the story where he regenerates into Eccleston and encounters his previous self. Just to make things confusing.