Actually, it's not even remotely close to the same thing.
See Invisibility, it doesn't work.
Invisibility Purge, it doesn't work
Uncanny Dodge, it doesn't work
Blindsight (feat (druid) or ability (Sacred Fist, creature), it doesn't work
In melee, blindfight prevents it from working.
WRT to the slightly different matter of flanking, flanking is much more easily mitigated. Characters may prevent flanking by moving, standing next to allies, etc. In most cases, that at least forces the rogue to move around for the flank--possibly provoking AoOs if he hasn't maxed out tumble and certainly limiting the rogue to one sneak attack (possibly two with a speed weapon).
For the bluffing rogue (assuming 16th level since it's a 10th level prestige class ability) the rogue is likely to have a minimum +21 bluff. Your standard fighter or monster opponent has +0 sense motive. He can roll a 20 and the rogue a 1 and the rogue still wins. A character like my Living Arcanis fighter/barbarian/cleric who maxed out Sense motive as a cross class skill? At level 16, he's only got a +9 sense motive and will usually lose.
In fact, before 3.5, Rogue and Bard were the only classes with Sense Motive as a class skill. In 3.5e, it's been added to the paladin skill list and, for all I know, it's added to the cleric list too (I'm not saying it is--everything I know about 3.5 I read online; it would just make sense). Still, the list of opponents vulnerable to bluffing is much much much longer than those vulnerable to improved Invisibility.
And WRT to the dagger or kukri being suboptimal for a rogue--not really. They're both optimal for gnome and halfling rogues. And for human and other medium rogues, they average only one point per round less than shortswords or rapiers and are easily concealable. For a character that gets most of his damage from sneak attacks, that one point is pretty much irrelevant.
Majoru Oakheart said:
Yes, but with the wizard casting an improved invis on the rogue and using a bow you can basically already do the same thing.