Widespread adoption of route numbers really took place during the 1950's, as the remaining streetcar routes were all converted to buses. Prior to then, except for the "Through Routes", route numbers were used internally only, for accounting purposes. The first transit route maps showing route numbers were issued in the early 1950's.
Some logic is almost always used when a transit system first devises a route numbering system. For example, the Toronto Transit Commission originally numbered its bus routes by route name in alphabetical order. But over the years on any transit system, service changes will include new routes and discontinued routes. New routes might be assigned numbers higher than the original numbering series, or numbers vacated by discontinued routes. Eventually much of the logic is lost, and a route number becomes meaningful mainly because people have known that route by that number. Chicago is no exception.
One can see some logic from the following groupings of CTA routes. Exceptions include routes serving numbered streets on Chicago's south side, where the route number is usually the same as the street number. The highest numbered streetcar route originally was the 81 Lawrence route, routes 82 and above were originally created as bus routes.
Although briefly, route numbers 82 and 84 were assigned internally to two streetcar routes added after the basic route numbering system was adopted. But both routes were later combined into other routes. Route 82 was on Devon, combined into Broadway route, now part of 155 Devon route. And 84 was on North Ashland, combined into 9 Ashland route.
After the Chicago Motor Coach Company was acquired by CTA in 1952, most CMC routes were assigned new CTA route numbers which were 100 higher. CMC route numbers had existed since 1923, originally with lower numbers on the south side, and working clockwise through the west and north sides towards higher numbers.
1-23 Original "Through Routes"
24-54 North-South routes, higher numbered routes further west
55-62 Routes operating on diagonal streets
65-81 East-West routes on north side, higher numbered routes further north
82-99 Newly created bus routes
100-119 Far south side numbered streets, later Dan Ryan rail feeder routes
126-158 Chicago Motor Coach routes, 100 higher than original CMC numbers
170-174 University of Chicago routes, created in 2000
200-206 Evanston routes, created in 1973