I wish they'd tied Punisher's ending in with Deedee and Elektra's a bit more. He just sort of shows up in the final fight like "Well, I already finished my thing, but there's still fifteen minutes left in the episode so I guess I'll shoot some Ninjas or whatevs".
Overall I really liked it, though. I thought the first season was OK, but it never quite boiled my potato. A big part of it was Vincent D'Onofrio being a ridiculous ham, doing his best Cookie Monster impression in an otherwise very down-to-earth, gritty thing, but this season played much looser with the realism. When Ninjas are pouring out of holes in the walls, Private Pyle hamming it up doesn't stick out so much, and I was actually disappointed he didn't get more screentime. Punisher and Elektra just about stole the show, and D'Onofrio's brief scenes were fantastic.
Biggest problem for me was the poorly-explained mumbo jumbo towards the end. I don't understand what Elektra being the Black Sky is supposed to mean. Does she have secret superpowers? Is she going to explode? Is there some chemical in her blood they want? No idea. Also, what was with the big hole? Did I miss something, or did nothing ever come of that?