If you think hydra was defeated in the first 5 minutes of age of Ultron you missed the point of the winter soldier. Hydra had figured out that direct combat wasn't their best approach and opted to play chess instead of checkers. In the mid credit scene of tws they even state they are going to let the avengers take out some of their bases while they work on bigger plans. While they didn't intend to lose the mind gem that was never meant to be the end of hydra.
While I don't think hydra created the registration act I wouldn't put it past them to take advantage and use it to turn the avengers against each other since they can't beat them, use a divide and conquer strategy.
You also said they had no part in the civil war comic, which is true but they did take advantage of the aftermath to shoot Captain America as part of a larger plot. So without knowing exactly what part they will play saying the movie will be lame because they are in it is premature.
What a cliffhanger! I wonder what character will show next in hydra only to be defeated in 5 minutes. Im on the edge of my seat! I cant wait until that huge cliffhanger of them being mollywhopped with no effort is shown again. Quisilver is dead and scarlett witch is an avenger. Their is no cliffhanger except findining bucky whos seen not being a part of hydra any longer and is clearly working with cap in the third film,.
civil war gonna be lit