^Screw the theorheticals, by sending an empty train every other cycle thanks to T:STR's "not permitted to skip" pre-show, Deja Vu probably does have a better capacity.
Ninja may not be the scariest or most popular ride in the park but it signifies one awesome aspect of the mountain, it uses the terrain to it's advantage throughout the circuit (which has always set this park apart from a lot of others). Also, it was one of the first "big coasters" for my brother and I when our parents started taking us to Magic Mountain way back when, and we LOVED the hell out of it! No doubt the young'n's these days probably feel the same, and IMO if there's any kind of "family coaster" list of the park, Ninja should be on it.
I also think Deja Vu is one of the sickest, scariest rides at the park, in the top 3 with X and Tatsu. When you look at that top 3, that's a serious list of intense rides that are VERY unique in coaster type, are not for the faint of heart, and they're all at one park. Even if you don't like the ride, you gotta admit, its pretty unique to have a single park which offers such a variety of coasters.