bondage fairies
what that manga is all about.
"Bondage Fairies"... the title says it all, really :O
*ahem* That aside, I like where you're going with this. More indie game characters should have legs like that!
Regarding her standing idle pose, the new one is an improvement, but she still just doesn't look ready. She doesn't even have her sword out! She should either get that steel out and start doing some sweet ninja poses, or if you don't want her to be running around with a drawn sword, she could have her hand on the hilt like in the Scene 1 image, ready to draw it out in a flash, iaijutsu-style (in fact I think Ryu does this in the old Ninja Gaiden games).
As for her climbing-up animation, I think it would look better if she ended in a crouch, rather than just standing straight up as soon as her feet land. Take a look at how Ayame gets over walls in this
Tenchu 4 video, might give you some ideas. Another idea might be to have her do something flashy like a flip or a handstand or something.
Other than that my advice is to play lots of ninja games for inspiration. Shinobi III, Strider, Kaze Kiri, that sort of thing. Also it probably wouldn't hurt to watch Jubei-Chan for cute girls wailing on people with katanas.