Jekyl has to analyze the transformation from the perspective of a scientist whose project was aimed to separate the duality of man's character. Yet, he only succeeded in accentuate them and bring them out in the open at will. However, it is not that he likes Hyde or not, it is the fact that he has come to the sad realization that the inner nature of humanity is dual: We are BOTH good and evil, good and bad, caring and careless. It is more human than people want to admit, and it is indeed something acceptable. He was saddended, however, that in his case he could not naturally experience the normality of shifts and change...he took it to an extreme.
Perhaps it is best explained in this quote, when he gives his version on the entire thing, in a letter on Ch. 10
It was on the moral side, and in my own person, that I learned to recognise the thorough and primitive duality of man; I saw that, of the two natures that contended in the field of my consciousness, even if I could rightly be said to be either, it was only because I was radically both; and from an early date . . . I had learned to dwell with pleasure, as a beloved daydream, on the thought of the separation of these elements