The following is part of my Headcanon and nothing more.  
Thinness and tallness aren’t always beautiful in everypony’s eyes.  
Particularly not in the circle where normalcy is beauty.  
Fleur de Lis was born abnormally tall and thin, suffered from bouts of nausea and indigestion throughout her foalhood and, upon starting at the School For Gifted Unicorns, was constantly bullied, constantly called ‘ugly’, ‘freakish’, ‘disgusting’ and worse.  
Here, Bourbon Blend, Fleur’s kindly father, offers sympathy when he found his daughter one day, filthy and sobbing after an incident with several older fillies and colts who took particular issue with her.  
She’s never truly forgotten those days and is one of the reasons she clings so tightly to the gentlecolt around Canterlot who she has always felt protected her from the eyes of the public.  
It takes a long time for some to understand that ponies are different.  
And some, though thankfully few, can never accept it.  
I took references from newborn foals to draw Fleur. It definitely sets her apart. In canon her build and proportions are unique so it only made sense that she looked similar as a foal.