system
Given the following post, respond as if you're commenting on Reddit:
human
[MCU] Spoilers - Connections between Iron Man 3 and Captain America 2

So after watching The Winter Soldier today, I was struck by a thought. Was Aldrich Killian's A.I.M. funded by Hydra? 

I feel like Hydra would have been extremely interested in Extremis as a potential replacement for the super soldier serum. Additionally, Killian's plan to install a puppet president seems like something that would fall directly under Hydra's overall plan for "control". In the Winter Soldier, President Ellis was an Insight target, so it makes sense that this may not be the first time they've tried to take him out.
gpt
In agents of shield the clairvoyant continues research on the super soldier formula from Ironman 3 (the centipede project). It's later revealed that the clairvoyant is actually a shield agent who works for hydra. This would seem to imply that hydra was funding it from the start.
Tl;Dr Yes.