I would have agreed with you if the HYDRA story arc had ended in a manner that I would have found enjoyable.
The problem, though, is that it's ended more than once. Hydra's been resurrected and brought down more times than it needed to be. I know that's their thing from the comics -- "Cut off one head and two more take its place" -- but I would've been content if it had stayed defunct after the events of
Age of Ultron, if Malick's group had been something separate unconnected to Hydra.
I don't like stories about pervasive, all-encompassing conspiracies, because they don't make any sense. If the group is that large and that ensconced everywhere, why is it even a conspiracy? The only reason to hide is if you don't already have power, if you're in a position of disadvantage. Sure, people in power can try to pull off conspiracies in secret, like Watergate or Iran-Contra, but they don't hide the basic fact that they
are in power, and because they're in power, they carry out the bulk of their agendas openly.
Plus, of course, as those examples show, real conspiracies tend to get discovered. Leaks happen, investigations happen, conspirators have pangs of conscience or make mistakes or get better offers. The larger and more pervasive a conspiracy, the more impossible it becomes to keep it secret indefinitely. So it's silly when fiction insists on having vast, far-reaching conspiracies that have managed to remain viable for hundreds or thousands of years.