I have seen this debate come up and I have to agree with one side whole heartedly:
The ninja should not get his own list of "tricks" that Rogues can not have.
The Ki pool could reactivate once per day talents with a spend but things like vanish, shadow clone, and the bombs it just isnt fair to give them only to the ninja when a Rogue could just as easily fit the description of those abilities (many of which are non ninjas in pop culture and literature that do).
My stance is that all the tricks should become talents and the ones that require a ki point to use again (or at all for a few such as Ki charge) should just become once per day talents that any rogue could do, with the option of prolonging them with a point of ki as a ninja.
It simply does not make sense to limit talents to an alternative class, and baring it from the parent class.
The Devs are quoted as saying that Alternative classes are just big archetypes, but archetypes dont give you a whole new set of ability choices (rage powers for instance don't and cavlier orders dont even for the samurai).
Why put the wall there at all and over complicate a basic archetype (it is far less complicated than some archetypes and replaces less abilities yet it is an alternate class....)
also on a side note one of the biggest reasons why I hope they change the ninja from an alternate class to an actual archetype:
I would love to combine other archetypes with the ninja with ease and without reprinting archetypes for specifically the ninja.
Making the ninja an archetype opens up doors where as singling it out is closing many.
We've only seen one complete alternate class from Paizo so far, and as it stands this whole "some things are only available to the alternate class" is pretty following the same trend as the Antipaladin. Check out the spell list, which I would equate to the rogue talents.
Needless to say I agree with the OP. The tricks need to go there is no need to have a "super talent list" and a "Lesser talent list" which is what we have now. Many of those are space wasting reprints or better talents that are not just ninja tropes. They make it harder to support and rob space from the rouge for no reason on top of being the only archetype/alt class to disallow others of the same class , new class talents.
I also agree on it being an archetype, it changes 6 items and has a word count of 799 words without the unneeded new tricks. That is less then some archetypes we have now.
We've only seen one complete alternate class from Paizo so far, and as it stands this whole "some things are only available to the alternate class" is pretty following the same trend as the Antipaladin. Check out the spell list, which I would equate to the rogue talents.
While I gather your point it is not the same for two reasons:
One the spells the antipalladin gains are actually the exact opposite spells just for evil (bane instead of bless and so on)
Two the two are two sides of the same coin with only alignment differences which is the only reason they differ at all (though small in actual power level)