Something to think about:

 

Leon and friends are likely still doing their best to clean up Radiant Garden. It's likely that, sooner or later, they're going to be checking around Ansem's old lab. And they're going to see Even, Aeleus, Dylan, and Ienzo are back on their feet. How do you think Leon is going to react to seeing the Organization members back and running, keeping in mind that they're responsible for creating the Heartless and screwing over the city and its people? 

 

If nothing else, it would be an interesting side plot to watch unfold in KHIII.

I could see a misunderstanding happening and Leon tries to attack them. Maybe Axel could even be there at the right time and you have to hold off Leon or fight him and after that Axel explains things.

never thought about that...

Would Leon even recognise them as Organization members though? Because the only person still wearing his coat out of that group is Lea/Axel and Leon has never met any of those members before as far as I'm aware. Therefore Lea is the only person at risk of being mistaken as a bad guy and in DDD we know that he went to Merlin to learn how to wield a keyblade and since Merlin currently lives in Hollow Bastion/Radiant Garden and is in close connection with Leon it is possible Leon has already been informed of Lea's allegiance with Sora. 

Would Leon even recognise them as Organization members though? Because the only person still wearing his coat out of that group is Lea/Axel and Leon has never met any of those members before as far as I'm aware. Therefore Lea is the only person at risk of being mistaken as a bad guy and in DDD we know that he went to Merlin to learn how to wield a keyblade and since Merlin currently lives in Hollow Bastion/Radiant Garden and is in close connection with Leon it is possible Leon has already been informed of Lea's allegiance with Sora. 

 

He hasn't seen them as Org. members, but he probably did as a kid, and he will question where they have been for 11+ years.

He hasn't seen them as Org. members, but he probably did as a kid, and he will question where they have been for 11+ years.

Well I guess so.

Well Leon never seen them as Org members and such so he will probably wonder who they are and how they got there, but remember that Lea went back to Radiant Garden at the end of Dream Drop Distance so he could've talked to Leon about them and such so who knows

He hasn't seen them as Org. members, but he probably did as a kid, and he will question where they have been for 11+ years.

Well he has seen them but they all had their hoods up, so he still wouldn't recognize them as the Organisation. But I'm guessing Ansem's lab is now a restricted area, so he'd probably be suspicious of any unfamiliar faces there. If the're still loyal to Xemnas this could give us a reason to return to Radiant Garden in III. Alternately, if they realized that Xemnas lied to them about Kingdom Hearts being the only way to get their hears back, which they probably have seeing as how they've returned as whole beings without obtaining Kingdom Hearts, they may even join the Radiant Garden Restoration Committee. (They need new business/membership cards)