I think there should be a ninja/alchemist prestige class in ultimate combat.
It would make some sense. They could use flashpowders and poisons more effectively and use their potions to turn invisible. Then tack on some extra unique abilities to top it off.
I've been thinking about the prestige classes and multiclasses
that will already work, myself.
Ninja/sorceror --> arcane trickster works well
Ninja/monk allows for ki stacking and a possible shuriken focus
ninja/shadowdancer is less redundant than rogue/shadowdancer, and a way to pick up evasion earlier. The shadow buddy also fits the theme better.
ninja/assassin on the other hand, isn't terribly good.
They could bring back the Ghost-faced Killer from 3.5 Oriental Adventures as well as some of the other PrCs from there. But Paizo could also take the route of using feats to make multi-classing easier like the Martial Stalker and Ascetic Stalker in the Complete Scoundrel.
Well, if You're going 3.5, I think ninja/dervish would be super fun. With things like wind stance and fast tumble, I think it would be great fun.