Here's an idea: Give the Ninja some sort of choice in it's specialization. You can go straight sword (ninja-to) and get interesting things from that, or you can shuriken spec and get completely different stuff, or you can go katar spec and get other things, or short bow, bla, bla, you see?

Also, there's nothing wrong with ranged flurry, as long as it's handled right. Flurry's mostly just bad because of medium BAB. So instead of doing it exactly like Monk flurry, do a rewrite that makes more sense. An additional attack with thrown weapons at your highest BAB, and no penalty. The max range could be 30ft so it isn't crazy good.

I also think Sudden Strike was totally fine. Hmph! I like that you were trying to focus it on striking from the shadows. That makes sense to me. But if you want to emulate Sudden Strike while staying different from Sneak Attack, again, write your own new ability that is similar.