Re: What villain should be pulling Winter Soldier's strings?
How could Skully be pulling the strings, anyway?
MCU timeline so far:
Bucky: survives the train raid in WWII, unbeknownst to Cap or any of the allies. Most likely picked up by HYDRA, since they were deep in HYDRA territory.
Red Skull: goes almost immediately (within 24 hours of the train raid) to the bomber, where he is whisked away to Godknowswhere by the Tesseract.
Arnim Zola: captured by the Allies, and forced to betray HYDRA. With Skully and Zola gone, HYDRA apparently collapses, and/or goes underground, taking a captive Bucky with them.
So, most likely, Bucky is abducted and brainwashed by FORMER elements of a HYDRA that has collapsed and/or been forced to go underground, with Red Skull and Zola missing.
That makes the puppetmaster for Bucky most likely to be a former HYDRA loyalist, like Zemo or Von Strucker or Madam Hydra (Viper). Whether or not that villain keeps HYDRA alive, or goes renegade to form his own outfit, remains to be seen. (I could easily see Zemo or Viper abandoning the Nazis at the close of the war and turning their "idealism" to Stalinist Russia instead during the Cold War, thus bringing the classic Soviet background to WS into play.)
As for AIM: no. IM3 has proven that AIM is *not* what you guys think it is. Forget little mad scientists in beekeeper helmets: AIM is going to be an above-board tech company that's a front for a more sinister organization.
THE COTTON AVENGERS
...They move like slick cotton on oil.