Why do so many countries have a super insignificant city as their capital?

Most of these countries have those capitals for various reasons with the main one usually being to have the capital in a more centrally located part of the country.
I'm originally from Pakistan where the capital was Karachi until 1967 when Islamabad was built to replace it. Karachi today is the largest city in Pakistan in terms of population with about 15 million residents. It is also located on the Southern coast of the country which gives it a major port for trade but it is far from other major cities and population centers.
Meanwhile Islamabad is in a more central location within Pakistan and is relativley close to other major cities like Lahore, Peshawar, Abbottabad, and Rawalpindi. This gives the national government and any agencies more centralized control.

It’s a little thing called the passage of time, where economic factors ebb and flow over time.

These countries should count themselves lucky they don’t come from a country where one city has such a stranglehold on a nation that nobody else gets a look in, like mine.