Note that SSN's capstone requires activation (including the Negative Level), so it's at worst an even trade, and you still get a new Maneuver Readied along with Flurry, Unarmed Attack Bonus, AC bonus and speed bonus from it. Oh yeah, and full initiator level. I find it very much worth it, especially since SSN 10 is epic ready. And really, the final ability is incredible, +4 on all attacks with shadow, the ability to heal yourself while evinscerating opponents with your insane Unarmed Damage and penalties to EVERYTHING. Hide bonuses, immunity to criticals, mind-affecting and so on... But yea, if not using fractional BAB*, I suppose losing a point of BAB is painful.
*[rant]Which is really like it shoulda been in PHB in the first place if the lazy effers didn't eff it up with a system that basically just effs multiclassing in the eye, which specifically is the major new feature of 3.X! Effin' effers; they effed saves up too, the bastards. Thank Wee Jas for UA and SRD making the variant commonly available.[/rant]