Here is what Lord Shiva tells while giving Pasupatastra to Arjuna:
Bhava replied, 'O powerful one. I will give to thee that favourite weapon of mine called the Pasupata. O son of Pandu, thou art capable of holding, hurling, and withdrawing it. Neither the chief himself of the gods, nor Yama, nor the king of the Yakshas, nor Varuna, nor Vayu, knoweth it. How could men know anything of it? But, O son of Pritha, this weapon should not be hurled without adequate cause; for if hurled at any foe of little might it may destroy the whole universe. In the three worlds with all their mobile and immobile creatures, there is none who is incapable of being slain by this weapon. And it may be hurled by the mind, by the eye, by words, and by the bow.'" [VanaParva Chapter 60]
If Vasavi Shaki was ultimate then Indra would have remained unconquerable with the aid of that weapon. But it was necessary to make use of that weapon to Karna as he had received it as return gift from Indra and to keep word of Indra it was necessary to destroy one thing by the help of that Shakti. Here is what Indra says while giving it to Karna;
Hearing this, Indra said, 'As thou, O
Karna, art bent upon observing the truth, thy person shall not be unsightly, or shall any scar remain on it. And, O thou best of those that are graced with speech, O Karna, thou shall be possessed of complexion
and energy of thy father him self. And if, maddened by wrath, thou hurlest this dart, while there are still other weapons with thee, and when thy life also is not in imminent peril, it will fall even on thyself.'
Karna answered, 'As thou directest me, O Sakra, I shall hurl this Vasavi dart only when I am in imminent peril! Truly I tell thee this! [VanaParva Chapter 308]
So to keep the above words of Indra if Karna used in such circumstances then it was necessary that one target gets destroyed.
Furthermore Pasupatastra is not a simple weapon which is to be hurled to mortals. Here is what Arjuna says :
Then the god Tryamvaka said unto me, 'I will give. O Pandava, my own weapon Raudra shall attend upon thee.' Thereupon Mahadeva, well-pleased,
granted to me the mighty weapon, Pasupata. And, having granted that eternal weapon, he also said unto me, This must never be hurled at mortals. If discharged at any person of small energy, it would consume the universe. Shouldst thou (at any time) be hard pressed, thou mayst discharge it. And when all thy weapons have been completely baffled, thou mayst hurl it.' Then when he having the bull for his mark, had been thus gratified, there stood manifest by my side that celestial weapon, of resistless force capable of baffling all weapons and destructive of foes and the hewer of hostile forces and unrivalled and difficult to be borne even by the celestials, the demons and the Rakshasas. Then at the command of that god, I sat me down there. And in my very sight the god vanished from the spot.'" [VanaParva chapter 166]
Then what is the use of possessing Pasupatastra?
Just having knowledge of invoking it is sufficient to make a person victorious. One doesn't need to use it. Here is what Lord Krishna tells to Arjuna when Arjuna vows to kill Jayadtatha next day:
I tell thee that the sun setteth quickly.' The bird-bannered Krishna hearing this cause of Partha's grief, touched water and sat with face turned to the east. And then that hero, of eyes like lotus leaves, and possessed of great energy, said these words for the benefit of Pandu's son who had resolved upon the slaughter of the ruler of the Sindhus, 'O Partha, there is an indestructible, supreme weapon of the name of Pasupata. With it the god Maheswara slew in battle all the Daityas! If thou rememberest it now, thou shalt then be able to slay Jayadratha tomorrow. If it is unknown to thee (now), adore within thy heart the god having the bull for his mark. Thinking of that god in thy mind, remember him, O Dhananjaya! Thou art his devotee. Through his grace thou shalt obtain that rich possession.' Hearing these words of Krishna, Dhananjaya, having touched water, sat on the earth with concentrated mind and thought of the god Bhava. After he had thus sat with rapt mind at that hour called Brahma of auspicious indications, Arjuna saw himself journeying through the sky with Kesava. [Drona Parva Chapter 80]
Thus, one doesn't need to hurl Pasupatastra, it's rememberance alone is sufficient.