All 3 of the Netflix seasons so far have had the problem of being too long. Cut a few episodes from each and they'd be a lot better. That said, the stuff that was really good in S2 of DD was anything involving The Punisher. The ninja stuff was completely at odds with it in terms of tone and goofiness (not to mention it didn't gel with the Punisher stuff very well at all). I am not sure how you really fix that though considering the goofy ninjas have always been a part of Daredevil and were always going to be a part of the show. I think if that was the focus of its own entire season and The Punisher was the focus of its own entire season then it wouldn't have felt as off as trying to mash them together.
With JJ it's like they dropped the really great Noir tone a few episodes in and kind of let the story get away from them. The "Nuke" stuff was also alarmingly bad and seemingly just there to set up the character for future seasons/The Defenders maybe?
I feel like both of these shows have a big problem with their supporting characters, with only the antagonists (Kingpin, Punisher, Kilgrave) being real standouts.
I have high hopes they'll keep improving though. Luke Cage is looking great and we don't have long to wait to see if it will avoid the same pitfalls of the others or not.