I don't agree that using Hydra ties the two films together as the Hydra shown in the first movie is not the same as the Hydra shown in the second movie. In the second movie, Hydra is what the plot demands, rather than a continuation of Hydra from the first movie.
Hydra in CA:TFA was an organisation of rogue Nazis that eventually amassed greater power than Hitler, due to the fact they had loyal troops and some very competent scientists. As they're shown in the movie, they don't have three heads such that if you cut one off they grow back fine -- they have one head (Red Skull) and one assistant head (Zola). Zola betrays Red Skull because he thinks he's going nuts, Red Skull is killed off (probably), and the body of Hydra is destroyed in an battle scene.
The Hydra shown in the second movie is a completely different organisation.
- In the first movie they are Nazis, and everybody in WWII German elites were German ethnic nationalists, even if they did not support going as far as Hitler. In the second movie, Hydra is run by Americans.
- In the first movie, Hydra is simply the hand of the Red Skull, in the second movie, Hydra is its own organisation and somehow we are to believe it was always independent of the red skull.
- In the first movie, Red Skull wants ultimate power for himself, in the second movie, Hydra is about bringing order to the world.
- In the first movie, Zola became a good guy, in the second movie, he was a mischievous bad guy all along.
Since Hydra in the second movie is a totally different organisation from Hydra in the first movie, using the same name for the shadowy villain does not do a great job of tying the two movies together.