Ok, so updated things I've gotten so far, thanks to help and tracking down the monk handbook from the old wizards forum.
Invisible Fist: Trade Reflex for invisibility for a round, one out of three rounds. A nifty trick, very Assassiny, helps with the rogue side getting sneak attacks. And, well, very flavorful. If I go nine levels into it, also gain essentially permanent blink.
Wall Walker (Dungeon Scape): Running up walls could be fluffed as parkour or what not, very Assassin's Creed and also in tune with the character concept!
Dark Moon Disciple (Champions of Valor web enhancement): Trade still mind for Darkvision 60ft (awesome, although I was contemplating getting shadow-walker), Total concealment in any condition over than full daylight at 7th! (does this allow you to make hide checks, ala Hide In Plain Sight!?), and shadow jump flavored dimension door instead of abundent step.
Useless baggage still left: Can't get the armor bonus in light armor, although I suppose armor isn't entirely necessary, its still nice to have. Flurry of blows still can't be used with hidden weapons and daggers/shortswords/rapiers. Unarmed damage won't be used (except if snap kick is taken), Purity of Body is still relatively useless.
Other options: I recently took a look at the Slayer, and it seems like it could certainly make for a good pair on the gestalt. Near full psionic progression, good BAB (makes up for the 3/4th on the left side), a nondetection on steroids (what more can you ask as an Assassin?) and permanent mind-blank essentially. Going psionic won't really make up for the feat issue, but its a potential option. Also, why he'd have a prestige class so talored around killing Mind-Flayers is an issue, when he's an assassin. Alternatively, if the DM rules that Kung-Fu Genius could be applied to swordsage, it could also work. I don't know how I'd make it different from my previous shadowlord//swordsage, though.