The ninja IS better than the rogue. By a mile.
The ability to detect magical traps is usually hardly ever put into use, and as the ninja can find mundane ones, you won't miss it terribly.
Evasion is nice, but not a must-have unless your GM loves throwing AoE spells your way.
The weapon selection and the ki powers are so much better than anything the rogue has to offer.
He is, in a nutshell, what the warblade was to the 3.5 fighter in my mind. Just better at everything that matters, with additional unique powers.
Even if you aren't into powergaming... Ninjas are just COOLER.
Are traps and the ability to dumb cha the only reason to select a rogue over a ninja?
The ninja ki pool (smoke bombs, invisibility, mirror image) looks a lot better than what the rogue gets.
The reason to take rogue over ninja is the ninja is Timmified Cheese, designed for powergamers.
Just on Principle, play a rogue.
Cheese? The class is ok, but not all that impressive, even with its invisibility ability that comes into play later in the game.
For being a trap monkey, there's the rogue.
For anything else, there's maste.. the ninja.
Scout/Thug/Knifemaster
I don't like Ninja though for many reasons...
Weapon Profs (same applies to Samurai),
Compare CHA Ki pool to Rogue Talent WIS Ki Pool,
so even though Ninjas can just get everything Rogues can,
it does not go both ways since Rogue Ki pool is worse.
In home games I would rule that Ninja Invisibility does NOT bypass See Invisibility, nor does Disappearing Dust.
The only reason to play a rogue at all is to handle traps. Ninja don't do that any better than alchemists. If you want to be a sneaky backstabber and don't need the trapfinding class feature be a vivisectionist. If you want to be sneaky backstabber with trapfinding you're still stuck with rogue.
Vivisectionist has a lot of things going for it (like extracts and mutagens), but I really think you're undervaluing rogue talents/ninja tricks. Invisibility/greater invisibility, Assassination, Underhanded, and Shadow Clone are some of my favorites.
anybody can use disappearing dust, and i just don't like that it bypasses SI, so i houserule it.
the rogue is the kobold of classes, it is weaker, but that's why some pick it.
Ninja is just the stealthy class thats about as powerful as the other regular classes, well at least as good as the monk.
Edit:@chaoseffect, the alchemist can have eternal improved invisibility, and 1 lvl dip into ninja can give him underhanded.
I forgot about Eternal Potion and that would be great if allowed, but I can't help but feel no DM would let me actually have it, though it may not be as OP as it seems as I have no idea the common capabilities of things that a party would be facing at level 16.
Totally play it as the Invisible Man though, bandages and all (given greater invisibility didn't just make all of them invisible as well ;o).
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Are traps and the ability to dumb cha the only reason to select a rogue over a ninja?
Mostly because the official rules in the d20 system nerf traps into being pointless wastes of time rather than anything approaching actual danger.
Ninja should have just been adding some more rogue talents. Maybe a minor archetype for people who feel the need to put "Ninja" on their character sheet officially.