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Subaru has several wishes which are revealed during various moments in X. The first is hinted at in X8 when he fought Seishirou at Nakano Sun Plaza. After creating a kekkai (barrier field) to protect the area, he explains that he has no interest whatsoever in the earth's future and that he's been looking for Seishirou in order to fulfil his "wish". What he meant by that was never clarified, but it's obvious that his wish has something to do with Seishirou one way or another. After battling each other for a while, Seishirou remarked that Subaru's "wish" must be to kill him and avenge his sister Hokuto. Subaru refused to say anything, indicating he's either reluctant to admit that Seishirou's right, or that his wish is something entirely different which he won't speak of. At any rate, it seems that "killing Seishirou" is too straightforward an answer. Subaru thinking process is complex, and it would be rather pointless for him to just kill Seishirou. So what does he truly wish for...?
In X12, Subaru takes on Fuuma after a brief battle with Nataku at Sunshine 60. Fuuma clearly had the upper hand, and for a second, Subaru saw just how much he resembled Seishirou. Since Fuuma is said to "resemble everyone and no one", he could sense that Seishirou meant something to Subaru, and by resembling Seishirou, he could distract Subaru and attack him. Poor Subaru let his guards down and Fuuma blasted him before blinding him in his right eye. His only explanation was that Subaru wished for it to happen, which is indeed true. 
Subaru, no matter how much anger and bitterness he felt towards Seishirou, has never got over the fact that the older man lost his right eye because of him. Whether it was a gesture of kindness or love, what it demonstrated was that perhaps Seishirou did feel something for him after all. Even if it's not enough for him to spare his life entirely, he just couldn't stand to see Subaru, who was so beautiful and innocent, get hurt. Subaru's tremendous guilt has weighed upon his shoulders over the years, to such an extent that he wished that he himself would also be blinded in the right eye. Even if he doesn't it appealing to lose his eye, his subconsciousness still wanted it to happen so that he can be levelled with Seishirou.