Yes, the Twins have a lot of interesting guys in the low minors, and it is certainly true that the Twins system might look a lot better in a year or two if these guys all develop like we hope. But the problem is that the Twins are not unique in this regard. There are probably 20 teams that have half-a-dozen or more interesting guys in rookie ball or instructional league, and each one can make the same arguement that there farm system will be so much better if these kids just develop like they hope.
But it doesn't really matter what other teams do. If, this season, a few of these things happen - not all - the Twins ranking skyrockets. Jay shows he can start. Stewart's krate/mechanics improve, Romero continues to break out at AA, Thorpe and Burdi get back on track after their injuries. And/or some of the 2016 draft class emerge. Frankly, none of those things are impossible and some, I think, are quite likely.
Ignoring rankings, the Twins AA rotation is apparently going to be Jay, Stewart, Gonsalves and Romero. That should be really exciting to follow. They all have flaws but all four have also been on top 100 lists this offseason.