I think a big factor is that Gondor was not subservient to Arnor, but an equal and independent country. It wasn't some kind of colony. Therefore, it wasn't obliged to keep Arnor militarily stronger than itself.
The second big factor is men. Fortifications and towers mean nothing if there are no men to defend them. Arnor could have had the strongest cities, but because of the divide between men they were all weakened from inside.
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You passed from under darkened dome, you enter now the secret land. - Take me to Finrod's fabled home!... ~ Finrod: The Rock Opera
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