I am hoping that Jarvis becomes Ultron because the best villains, like Stane and Loki, are those that have a deep personal connection to their nemesis. With Pym out of the picture (though I am hoping Whedon has Pym collaborating with Stark on the Jarvis AI), the Stark/Jarvis relationship is a terrific one to exploit. It will be quite chilling to have the voice of Paul Bettany coming out of a killer robot.
Whedon mentioned that Ultron will be going through upgrades during the film, so while he will start out with a transformed Iron Man suit, I think he's eventually going to end up in the big guy - the Destroyer armor. From the Avengers preview comics we know the SHIELD has the armor, and having Jarvis/Ulton transfer his conscious into this form is a much "cleaner" path to take than having him create a body from scratch. Indestructible armor is very difficult to come by, and SHIELD having one that somewhat resembles Ultron's comic book dimensions may be too convenient to pass up.