The stats show that he starts slow at every level, and then "figures it out"
I've said enough about Baez that I feel people know my opinion. But, what I will say is this is a fallacy not because what you're saying is wrong but rather because the implication is that "figuring it out" at A+/AAA means he will figure it out at the major league level. There's just no guarantee that will happen. Additionally, I've said this before but I think it bears repeating. Baez is undoubtedly one of the more physically gifted prospects in recent memory. However, raw talent only gets you so far. At the major league level most players are quite gifted. So, while in the minors you can feast on less talented players that's not always the case in the majors. The analogy I've used before is a pitcher with a dominating fastball. In the minors that works great because many hitters can't keep up with him. But if that's all you got when you get to the majors often times players like that will fail because at the major league level most players can hit a great fastball.
What we've seen thus far from Baez in my opinion is a player who has next to no polish and is relying mostly on his physical talent(bat speed/power). I forget whether it was the moneyball movie or book(maybe both) that talked about Billy Beane the player but to paraphrase a bit, he was the type of player that never failed long term and when he started to struggle he just didn't know how to handle it. Another analogy I've heard thrown around this concept was back when Mike Tyson was king of the boxing world it often seemed like he'd beaten people before the match started until Buster Douglas knocked him out and frankly he was never the same fighter. That's what I worry about happening with Baez. His natural talent has gotten him this far and he's never needed to have a refined approach to hitting. He now does need that.
It's possible Baez eventually figures it out but it's also possible he never does. Cubs fans above most others should realize this. Around 2 years ago Brett Jackson was hitting .175/.303/.342 with a 15.5%/41.5% walk/k rate in 142 plate appearances as well as decent defense in CF. Baez is hitting .164/.209/.350 with a 5.4%/41.9% walk/k rate in 148 plate appearances at 2B with negative defensive metrics although that doesn't mean that much this early. If you had to pick one without knowing the hindsight Jackson's numbers would seem the safer bet given that he was already walking at a high rate and at the very least playing good defense at a premium position. That's not to say Jackson was ever the better prospect or that Baez will work out the same way but if you're naive enough to believe this isn't a worry then look no further than 2 years ago where people undoubtedly were saying Jackson just needed more time.
It's fair for people to make the argument that not every prospect will come out hot. Erroneously people often talk about Mike Trout as the peak of playing amazing from the start when his first season in the majors he hit .220/.281/.390 . I and I assume others get that. What those people need to realize is the year following those numbers from Jackson he hit .210/.296/.330 9.5%/32.9% between three minor leagues and going into this season almost no one was mentioning him as a hopeful. That's how quick you go from next big thing to an after thought traded away for next to nothing. And like Beane/Tyson, once Jackson failed hard he seemingly lost his confidence. Frankly, none of us can know for sure at this point. But, if the cubs feel <x> player(s) will get them where they need to be and the cost is Baez I'd trade him even knowing his immense potential because where Baez is today and where Baez needs to be in order to be the player people think he can be isn't a minor tune up in AAA next year. It's a major change in his approach to hitting and as we've seen with Castro, even minor changes to approach can really mess with players.