You're not thinking about it too hard but rather not hard enough. Running an airline is, as you may have read somewhere, not always a profitable business. Overhead costs are high and margins are tight, to keep it short and sweet. Flight planning, the exercise of having aircraft and crews spread across your network so that both of these inputs have as little downtime as possible, and are constantly revenue-producing, is complicated and not helped by delays (mechanical and weather) and other factors which throw of the fine-tuning. No one has aircraft and crews just lying around waiting for something to do. Just think about amplifying your situation to the 100+ airport where your carrier operates.