From mere observation, the British realised the differences between the north and south of the country in terms of physical appearance, culture and sociological behavior. It dawned on them that the people of the south had more in common with their southern neighbours, i.e. Northern Uganda, Kenya and Congo.
But then the British also realised that despite sharing the hardships of their southern neighbours, the people of South Sudan were actually in a more dire condition. Inevitably, this lead the British - with the burden of history eating at their conscience - to think that uniting the north and south of Sudan would afford the southerners a chance for development.
The north at the time was more acquainted, more developed and a product of conquest by various empires throughout history.
This theory worked on paper.
The three British governors of the south at the time objected to this setup, and so did the missionaries. In turn, they offered a different approach. They proposed that a unified Sudan should grant Southerners a "special status". This special status offered Southerners privileges in access to education and the like, up to the point where there would be a balance - in terms of development - between the north and south.
So in 1948 this "special status" was voted for in parliament - in which there were Southern members - in the central government in Khartoum. However, in kicking off a tradition of failed political strategies, the "special status" was scrapped in January 1956.
If, in 1948, there existed a semi-competent politician among the northerners, the South would've been given independence there and then. However, the outlying problems back then would've prevented any attempts at development for the South. The myriad of tribal affiliations, illiteracy and general lack of professionals are just a few.
So it seems the South could have easily gained independence 63 years ago, but the tribal differences would've had an egregious effect on the country. Now however, there seems to be a sense of unification. The Southerners are proud to be a nation, not a tribe. Sentimentally, independence is definitely worth the 63 year wait.