HYDRA doesn't want to wipe out humanity; they just want to wipe out superheroes. And then corner the market on superpowers for their own brand of villainy. In other words, ultimatum to (un)registered gifted: join HYDRA, or die.
Ultron would be the ideal tool for HYDRA to enact The Zola Algorithm.
In other news, anybody keeping up with the news from Marvel today about that girl from The Middle, Eden Sher? The news involves Tweets about an 80-lb stack of Ms. Marvel comics....
Bingo.
My idea is that it was this computer software by Pym, long ago, who received help from Howard Stark. This program, perhaps Project Insight, could have been buried deep within shield's hidden files or something. After HYDRA's infiltration of SHIELD, they could have gotten access to this AI and tried to use it to deal with the algorithm.
Meanwhile, the software has a front row seat to all the political stuff going on with SHIELD vs HYDRA.
Tony could maybe have built a bunch of robot drones or something, but deep within SHIELD, he would find this software, this AI, and see that his dad worked on it. Tony already has trust in AI, so he brings it into the world..maybe modifies it, maybe doesn't. Now, we saw Cap's role in the politics of the winter soldier, and the role he had in the collapse of SHIELD against HYDRA could be viewed as a way to lead into the avengers sequel.
Ultron would have been watching and gathering everything wrong with supers, HYDRA, SHIELD, humanity, and the avengers.
This way, not only would Ultron come from the avengers we know, he would have come from basically all corners of the MCU.
Doing this would give the character much more presence. If some part of Ultron doesn't exist before the Avengers sequel, and if Stark is the sole creator of Ultron...the person who replies to this message first, mark my words...I will send you $40 via pay pal. screen shot it, put it in your sig, whatever.