Injuries and luck can play a huge role in here are my two cents. First is best prospect, second is second best etc. (also even with hindsight, these things are strongly subjective- Chamberlain vs Russell is even today an emotional subjective question, although I am sure everyone here knows the correct answer

)
1. Karl Anthony-Towns
2. Kristaps Porzingis
3. Myles Turner
These three have proven themselves. I'm p confident about the order too.
4. Embiid
If healthy, Embiid belongs to the first group.
5. Booker
He is very young, and already a good scorer. Haven't watched enough the Suns the last two years + IMO good bigs usually have a greater value than good guards because they are rarer.
6. DLo
Liked his first year, not so much what I see this year. He is good, but nowhere close where KAT is.
7. Mudiay
He is still a project. He has guts and he is athletic, but certain aspects of his game (esp. shooting) are still raw. As a prospect I would take him over DLo. As a production in the current year, I prefer DLo - mainly because of Mudiay's TOs and bad decision making.
8. Ben Simmons/Jaylen Brown
Too early to say. Simmons is a great prospect, but has not played a single NBA game. Jaylen Brown is athletic and smart but raw. I can see them both becoming better than Mudiay and DLo given time, but let's return to this question in a year from now.
PS Do I miss something about how the list was composed?
All-Rookie or All-NBA third team awardees not included.
KAT (2016 ROY), Porzingis (2016 All Rookie), Turner (2016 All Rookie second team), Booker (2016 All Rookie), DLo (2016 All Rookie). This is literally the 2016 All Rookie team, what do I miss?
Moreover, the less than three year criterion mentioned in the OP is met by several players not included here (eg Jokic).
Apologies if I miss something, but just going through it the list reads like a random selection of players the OP was interested in; I love Brown, but does he belong in the same conversation as KAT? And if we are going to include Brown and Simmons, then why not Brogdon, Ingram and other prospects from the last draft?