A few examples I thought of, where cities besides the capital held way more appeal to me personally -
Norway - only Tromsø and Bergen, not Oslo
Croatia - only Dubrovnik, not Zagreb
Tajikistan - only a remote region in the northwest, not Dushanbe
Poland - only Krakow and Wrocław, not Warsaw
Spain - only Malaga; not Madrid
Montenegro - only Kotor and Perast; not Podgorica
Edit: forgot about Malaysia - only Sabah in Borneo, not Kuala Lumpur
Laos - only Luang Prabang, not Vientiane