Pronunciation aside, I always found it rather perplexing that an academy on Galifrey would resort to using an alphabet from Earth of all places?!

That said I figured that the nickname, like nicknames on Earth, was given due to the Doctor's interest in this planet. Was Earth his thesis topic? Could explain why he took off in an old type 40 - the campus headline could be "Disgruntled honours student breaks in to near disused storage room. Takes equipment noone really knew or cared was there."

So then I was thinking why Theta Sigma? Time Lord society is Science and Math based. In maths (here on Earth anyway), theta is generally used to represent the unknown angle in a right triangle, capital Sigma is used to represent summation and lower case sigma to represent a standard deviation from the average. My take is that because the Doctor's views on Time Lord society were different from most other Time Lords, you could think of him as being at an angle to what is "right" in that society. Using lower case sigma, you could also think of the Doctor as not being average, in both personality and intelligence, he would be a standard deviation from the average. Hence Theta sigma.