Your question is indeed very reasonable. The answer lies in time being multidimensional?
I would encourage you to read the book "Surah al-Kahf and the modern age" by Sheikh Imran Hosein, in it's chapter one (page 21) the very same question has been asked.
You will find your answer in that chapter.
Because of the many supplications of the Prophet Sallallaahualaihiwasallam صلى الله عليه وسلم! He loved Madina and its people that he decided to die there! In a narration in Sahih Muslim, he said: (O Allah makes us love Madina as much as Makkah or even more!)
So it is even permissible to love Madina more than Makkah! It is the place where Islam was ...
Assalamualaikum! The importance of Medina can be derived from the facts given below:
The first mosque of Islam was built over there
The mosque of the Prophet (Sm.) ,i.e. the Masjid al Nababi was also built there
Rasulullah (Sm.) rests in peace there.
The 3rd one is the main reason why Medina is more important than Al-Aqsa and if you want to know the facts ...