I'm an experienced commissioner, but am curious to hear others' experience with drafting/protecting minor leaguers/prospects.
Currently we carry 40-man rosters (24-man active roster) and protect 15 each year. On draft day, the first nine rounds fill out active rosters and then the "Reserve" portion of the draft starts (16 rounds), at which point anyone not on Opening Day MLB rosters can be picked. So what typically happens is the first round of the "Reserve" portion turns into the top prospects round when guys like Longoria, Carlos Santana, Price, Wieters, Beckham, Jennings, Ackley, etc. have been drafted in the past (i.e. touted guys who began the season in the minors).
But ultimately unless you hit on an elite player (e.g. Longoria), you don't get much production from a prospect who plays most of the season in the minors while taking up a spot on your 40-man roster and you don't get rewarded because chances are he isn't one of your top 15 worth protecting at the end of year. Further, a player in the minors can't be released in order to sign a FA in our league.
So my question is how do you guys handle drafting of prospects/minor leaguers, carrying them on your team and potentially keeping them for multiple years? Do you have a separate draft? Do you have a "Farm" team separate from your Roto rosters? Do you protect them differently than big leaguers? I'd be curious to hear any input or explanation/opinions of your league's practices?
Thanks for reading.