Draw the line before you pick the cities
A good route is a line or a loop, never a star. Backtracking is the most common structural error in multi city trips, and every backtrack costs you half a day plus the cost of the leg.
Put your candidate cities on a map, find the sequence that involves the least repetition, and be prepared to drop the one that breaks the line. It will be there next time.

Let transport set the shape
Check the actual connections before committing. A three hour train is a different proposition to a ninety minute flight with two airport transfers. In practice, anything under four hours by rail beats flying once you count check in, security and transfers.
Open jaw flights, arriving in one city and departing from another, remove the single worst constraint in route planning and rarely cost much more.
Nights per city
Two nights means one full day. Three nights is the realistic minimum for a major city. Four nights is where a city starts to feel comfortable rather than surveyed.
Count travel days honestly. A morning train and an afternoon arrival is not a full day in either city.
Sequence for energy
Front load the demanding places while you still have energy, and end somewhere slower. Arriving home from a quiet coastal town feels entirely different to arriving home from a fourth consecutive capital city.
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