I'd say Lehtonen is the better goaltender and the better prospect right now. But I think a case could be made either way, for Fleury or Lehtonen.
However, who is better right now is of little importance in the grand scheme of things.
I think who ultimately is the better netminder will depend on the teams in front of them. Right now, both the Pens and Thrashers have pretty bad defenses. For a young netminder to have sustained success in the NHL, the teams in front of them will need to show more of a commitment to defense than they have thus far.
The Penguins had by far the worst defense in the league last year, but they have one of the better groups of defensive prospects around. They may or may not pan out, but there's alot of potential there. Also, the plans that the Pens have laid basically are for a defense-first team, based around Fleury. Aside from Malkin, most of their top prospects are two-way players or defensemen. Whether this Jersey-esque team ever comes to fruition is uncertain, but that's what management seems to want.
On the other hand, Atlanta has built an offense-first team; obviously based around Heatley and Kovalchuk, among others. They do have some young D-men that will soon step in, but will they change the philosophy of the Thrashers? I'm not so sure. In the past three years the Thrashers have had, at its highest, the 25th best defense in the league, although it's improving (but signing Modry doesn't help). I personally think Atlanta will and should play a run-and-gun style, but that might hurt the numbers of Lehtonen, and so also the general perception we have of him.
Obviously, getting solid goaltending will be perhaps the biggest step towards the Pens and Thrashers being better defensively. But Lehtonen and Fleury can't do it alone, at least I don't think.
Right now, Lehtonen gets the nod as the better prospect. But in ten years time, which is what the original question asked, things could change. How the Penguins and Thrashers improve their lacking defenses in the years to come could go a long way to determining who is the best goalie in the league.