This accomplishes many things.
1st. He is only 18 now and if you do the math, he will only be 20 in 2 years

2nd. It gives Flynn the opportunity to boom or bust. If he comes out CP3 sytle and dominates, than we have a valuable trading chip in Rubio. If he shows that he is just a decent starter, we can move him.
3rd. We have potentially 3 picks next year as well. Delaying for a year or two will give us the chance to build the best team possible to fit his style.
In two years we will have a team that is ready for an older and better Rubio to take over, that is built for him, and all this while Rubio will be on a rookie contract.