the difference is that the success of ninjutsu is based very heavily on other capabilities of a person. it's unlikely for anyone to land a chidori or rasengan on someone that's faster than them, but finger jutsu doesn't care. ninjutsu is only ever great when paired with someone who's already strong in some other regard like chakra capacity or reactions.
The same could be said for genjutsu. There are shinobi (even non-Uchiha) who are genjutsu resistant. Therefore I could just as easily say that genjutsu is only great when paired with someone who is potent enough in yin release to cast a powerful enough genjutsu to stop the enemy.
Besides, you are assuming too much. Attacking the enemy with an attack such as rasengan or chidori isn't the only way to avert the stab via ninjutsu.
You could use a spacetime ninjutsu like flying thunder god, kamui or amenotejikara to teleport and dodge the attacker (or phase through in the case of kamui)
You could use a barrier ninjutsu or even something like an earth style wall, a shield made of truth seeking balls or susanoo to block the attack.
You could use substitution jutsu or shunshin.
You could use a long range or widespread jutsu like chidori nagashi to fend off the attacker before they can even get close enough to you to stab you.
Etc...
The list goes on and on.
On another note, ninjutsu can be way more versatile than genjutsu at times since it can be used in practical situations as well (and not just battle).
Examples:
I could use shadow clones to multitask and have one clone do my homework, one clone pay my bills, one clone do my grocery shopping and one clone do my laundry while I just chill. Can't do that with genjutsu.
I could use water style ninjutsu to put out a fire from a burning building. Couldn't do that with genjutsu.
I could use Ohnoki's lightweight rock technique to fly and use that as a better means of transportation than driving in traffic. Genjutsu wouldn't do that for me
I could use creation of all things to create anything I want out of thin air for myself. Genjutsu won't suffice there.
See what I mean?