Yeah, I basically used Gez's cool little Ninja Monkey as the baseline for my variant Ninja Assassin. I tried to integrate more of what seemed Runesong's focus and abilities for the class, while trying to keep it reasonably balanced with a rogue, bard, or assassin (while keeping in mind that it's a fairly focused prestige class and thus deserves to be a bit more powerful in its focus).
As for some of the reasoning: I ditched Improved Evasion, Uncanny Dodge, Improved Uncanny Dodge, Mettle, and the full BAB progression for the simple reason that, as I saw it, the prestige class' focus was supposed to be a hit-and-run, get-in-and-hit-a-few-times-then-run-away-before-resistance-mounts kind of warrior. They're not supposed to stick around and slug it out with knights and samurai and bodyguards, not for more than a few rounds anyway, so they're not supposed to have solid defense, accuracy, or hitting power. They're supposed to use surprise, speed, and mobility to boost their accuracy and striking power for a few moments, then escape just as resistance is starting to build up, before their escape route is blocked or they get surrounded. They aren't supposed to stick around long enough to be dodging fireballs, suggestions, curses and such, and they aren't supposed to get surprised by attackers, they're supposed to do the surprising. That's what was in my mind when I threw together the class' stats. I kept the good Fortitude save to represent decent physical training and exercise, plus a degree of experience in resisting poisons and such.
I kept Ninja Sight toned down and short-lived for the sake of balance, but really, with access to bard spells they'll be able to cast Darkvision, See Invisible, and similar spells once they gain 2nd-level spells about halfway through the class progression. I figured they'd use Ninja Sight once they've made it close to the target and need to 'run the gauntlet' through the toughest area where they'll most need a clear sight of their surroundings and their target. Definitely it would be better to keep Gez's Nightprowler ability intact instead, but I just wasn't sure it would be as balanced given the various other abilities I gave them. I did forget that Runesong was looking for an Assassin progression for spellcasting ability, so by accident I just gave them straight-up bardic spellcasting progression; I'll fix that now. I may tweak a few other things in this quick check-over; I threw it together too quickly to check my books and remind myself how certain abilities work specifically, nor did I have the time to check it for balance at the time. I'm going to add Spot 8+ ranks as an extra prerequisite though, something I forgot before I hit "Submit Reply."