Here are a few ideas I thought up for season 2 story arcs.
1. Vanessa's in the wind. The FBI didn't arrest her, so she is free to make contact with Wilson's criminal associates in Italy (surely he has some). She expressed the desire for revenge against those who wronged her and Wilson, so maybe she hires an assassin to kill Daredevil. Maybe a Europe based assassin of the female persuasion. One with a Greek passport, perhaps.
2. The assassination falls through because Elektra recognizes Matt through the mask and refuses to kill him. Vanessa doesn't like this, and dispatches another assassin to clean up the mess and leave no connections to her or Wilson. This time an assassin with a penchant for thrown weapons.
3. The Hand seeks revenge for Nobu's immolation and a whole mess of ninja invade Hell's Kitchen. Matt is in over his head, so Stick, Stone (the mysterious man seen talking to Stick in episode 7, I think) and Melvin/Gladiator jump in to help out. Ninja Battle Royale ensues.
4. We get more info on Karen's secret. The one Ben discovered, but did not disclose. Skin flicks in college? Past drug abuse/convictions? The former drawn from the source material, the latter insinuated in the series.
I hope a couple of these stories do happen. It's gonna be a long wait for season 2.