As I understand it, each country can allocate its ICAO designators as it wishes, within the global scheme, thus the UK can arrange the last two letters according to its whim.
Despite initial appearances, the UK codes are logical, in an historic manner. With the relatively-crude switching systems available on the AFTN (Aeronautical Fixed Telecommunication Network) in the 50s and 60s, there was a need to keep flight plan addresses to a simple system. Thus, after the pre-ordained EG, the country was sub-divided into areas for the third letter -
A = Northern Ireland (A for Aldergrove?)
B = Birmingham
C = Manchester
D = Military airfields in SW England
etc, etc
The last letter indentified the specific location, with the added fact that the main AFTN unit in that area had the fourth letter the same as the third, eg EGKK, EGLL, EGTT.
In recent years the advent of software switching and better systems of data transfer have made the system somewhat of an anachronism, but it has been deemed too difficult to make wholesale changes. However, new airports like Sheffield (EGSY) do not conform to the original master plan.
Other countries, like France and Italy, have a very similar system, so we're not unique. I hope that this rather fact-laden reply does cast a little more light on the subject.