Regarding the question of whether we'll see Hydra again anytime soon, I think we will. I think it'll happen around the time of Age of Ultron. It may involve Bakshi and that guy who was seen with Strucker.
Except that Bakshi is a captive of Ward and 33, who are brainwashing him to do their bidding. His loyalties presumably won't be with HYDRA anymore. Although I suppose it's possible they might send him against HYDRA.
Still, I kind of suspect that the show is deliberately trying to avoid covering the same subject matters as AoU. They had to tie strongly into
The Winter Soldier because that movie was about SHIELD, but that created a lot of problems for the show and was difficult to pull off. In general, it would be safer and more freeing to avoid more than a token overlap with the movie -- which would be an incentive for avoiding anything AoU-related and focusing instead on the Inhumans stuff and the inside baseball within SHIELD.
Although on the other hand, Fury appears to play a significant role in AoU, and we're in the midst of a storyline that's heavily driven by Fury's legacy. So there may be a tie-in planned there. It's possible that the events of AoU will force Fury to come out of hiding and reveal he's still alive, and then that could have a decisive effect on the conflict going on between Team Coulson and Team Gonzales.
But I don't believe we're just going to see another crossover about HYDRA in the show parallelling HYDRA in the film, because that's what they did the last time. They probably want to avoid repeating themselves.