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Trapfinding just isn't that great in a game where traps have been nerfed to hell and other classes can do it just as well (Ranger archetype). Though this really depends on how you see traps in your game. Poison Use is a really nice ability to have when you actually use poisons, but I think it's a fair trade.
As far as ki goes, Rogues don't get to apply their level where the ninja does, does not get an extra attack, get half the bonus to speed when using ki to boost speed (rogues only get 10ft, where ninja get 20ft) does not get to use it to improve stealth, does not get a reduction on acrobatic checks, and must use wisdom (which most players don't bump up very high on a rogue, they'd rather have a charismatic rogue).
All the cool ninja tricks require ki, which the rogue will have very little of (about half as much as the ninja). The rogue gets the stripped down version of ki which requires them to have the wisdom of a cleric to actually be worth it.
A ninja can also take Evasion after 10th level as a trick, thus only really missing out on trapfinding.
And the 20th level ability (which to be fair doesn't come up in most games) is much better. They get the ability to become completely undetectable even by see invisibility, or even true seeing for 2 minutes, and with every sneak attack they can deal ability score damage (no saves). Where with the rogue's master strike the enemy gets a save which is determined by the rogue's intelligence.
What it really it just comes down to: Ninja ki > Rogue ki