The problem with the Punisher is that it's hard to make the character the focus of his own show. Especially when Netflix mandated 13 episodes per season. The comics are simple: Frank wakes up, kills very bad people in very nasty ways, goes to bed. For a TV show, that doesn't work. So you end up with a lot of filler with Castle working through his feelings. Usually by shouting angrily at someone.
Again, this is completely different from the comics, where Castle has the emotional range of a Vulcan on Xanax.
Bernthal nails the role, it's just that the character is best used in small doses. He was great in DD S2, because the a lot of his early scenes were just him fucking up bad guys. Yeah, he does get a few emotional scenes, for example the rooftop with Matt and later when he talks about his family. But those are outliers. For the most part, he's a flesh and blood version of the Terminator. A killing machine.