Even though he was allied with Orochimaru, Orochimaru himself seemed uncertain of Kabuto's loyalty which I found very interesting. To a certain extent it seemed almost like he was using Orochimaru. No one ever seemed to understand exactly what Kabuto was up to, and that made me think he always had a big end game of his own. I still hope that turns out to be the truth in some way.
Kabuto also showed an interesting side when he fought Naruto during the Sanin battle. He criticized Naruto for being naive about his power and also criticized him for relying too much on the Kyuubi's power. It was interesting though that Kabuto actually seemed a little bit pleased when Naruto was able to hit him with the Rasengan, it was almost like he was glad to see Naruto grow. Kabuto always seems to be amused, even when things don't go the way he expected. Another example, was when he confronted Naruto after he had began to merge with Orochimaru's body and gave Naruto his information about Akatsuki.
Kabuto is one of the only characters who has a strong connection to almost all of the major Protagonists and Antagonists of the series. He is closely connected to Naruto, Sasuke, Orochimaru, Danzou, Akatsuki, Obito, Itachi and even Madara. Kabuto was the first major villain to be introduced and he has played a part in almost all the major conflicts throughout the series. I think he deserves to play a big role.
I agree, that Kabuto shouldn't simply become "one of the good guys" I think Kabuto's change should be about him becoming his own person and seeking to obtain his goals in his own way. I want to see exactly what his old plans were and I want to see his new take on those plans now that he has been forced to reevaluate his life. I don't think it should have been a matter of him being simply good or evil. Kabuto like many of the best characters in the series, should be more complicated than that.