Hmm... I think I removed Two-Hander (those need to be redone I think. The method I'm using to track them isn't the most reliable)
Pin-Down not staying around is very odd. I swear sometimes RPG Maker has a mind of its own when it comes to skills.
Isabelle has no default skills, she learns them by eating Titan Fruits (unless you gave her titan fruits, then thats an issue)
and yes, the endings are a little broken currently. Sometimes they play nicely but generally they don't :(