If Team Ninja is known for two things, it's sex and violence, but that doesn't look like it's going to be the case going forward. Gamasutra has an article with interesting comments from Yosuke Hayashi, who took over as team lead after Tomonobu Itagaki resigned. He talks about how the tastes of the gamer audience have changed, and so making games that appeal to the more base aspects that the studio was known for under Itagaki (copious blood and huge, scantily clad breasts) and little else are a thing of the past. The team is apparently more focused on integrating games with emotion and reason; things that seem absurd when you consider things like the DOA Extreme games, but according to Hayashi, DOA5 is going to make an effort in treating the female characters as more than bouncy tits to gawk at.
And honestly, I can see where they're going with this. Like the story or not (and it should be noted that Team Ninja did not write the game's story), Metroid: Other M's narrative elements were deeply integrated into the gameplay to the point that there's a natural flow between the break in gameplay and the start in a cinematic. Similarly, Dead or Alive: Dimensions made the effort of retelling and tying together the stories of DOA1-4. The game wasn't entirely successful (for reasons I've laid out here), but it shows that the studio has started putting in more effort in bringing at least some level of depth to these characters. Ninja Gaiden 3 appears to be headed down a similar path, as well.
It'll be curious to see how this new direction works out for them. I had a feeling that without Itagaki at the helm, Team Ninja was destined to go in a different direction, and this is a direction I like. I hope it works out for them.