My top three draft picks (low 1st round, 1st round supp, and 2nd round) had little to no improvement last season.  They were all playing on my LoA team.  I'm wondering if coaching is the problem?  I noticed that all of my LoA coaches had low patience attributes.  Does that have anything to do with improvement?  Are there any coaching attributes that I should focus on when hiring my minor-league coaches?

The primary attribute and patience are what to  look for.

Prospects don't seem to progress normally in the first season.  That said, you're also running 15-16m in training so you're not going to get full physical development in the off-season.