It's an interesting development. J.A.R.V.I.S as an AI has been characterized as fairly powerful. Paul Bettany seems like he could step into the role of the Vision pretty well.
As for who actually develops Ultron? I think there are plenty of possibilities out there for how that might develop. Stark's tech hasn't been completely secure over the history of the Iron Man movies, or the Avengers. Stane got a hold of Stark's Mk 1 plans in the first Iron Man. Justin Hammer weaponized the Mk 2 armor, turning it into War Machine. Also, Vanko managed to hack that armor in addition to the creation of the Hammer Drones and his own Whiplash armor. Stark hacked SHIELDs computers in AVENGERS. One would think that it might also be possible for SHIELD to hack the Mk 6 armor when it was on the helicarrier. And in Iron Man 3 AIM managed to hack the Iron Patriot armor. Add all that up and Tony's armor has been somewhat less than secure.
But I think that some of what we saw in Iron Man 3 may be at the root of the Ultron creation story. After Tony works on the implants that allow him to summon the Mk 42 armor remotely, we see a scene where Mk 42 is assembled and has independently made it's way to Tony as he's sleeping. Perhaps what's next is that a new suit beyond Mk 42 becomes self aware, leading to Ultron.