You don't have to click on so many different level seeds for the
same plant when planting. I find it convenient. Other than that, I
haven't noticed any real difference with level 100. Though to be
honest, if you do bulletin board orders, they will ask for higher
and higher level seeds, slowly phasing out the use of lower level
seeds. Eventually, any other seed besides level 100 become
completely useless for the bulletin board when it asks for berries
/ seeds.