I have found, up to level 30 anyway, that small references to my starting city and the reputation I have achieved there occasionally is brought up in dialogue when it comes to returning there for another big quest.

I do get how you feel though, I too lucked out as someone else here, by wanting to be a Limsa Lominsa citizen and also wanting to main as a Arcanist/Scholar.

As others have said, after 15, you can ditch leveling your initial class and start somewhere else, but if you are mildly OCD or are a perfectionist like me, it'll prolly bother you!

Hope this helps.