Certainly plausible. Lewis also gets lumped in with guys like Miranda, Julien, Wallner (to an extent) ect. and that's not really apples to apples. I'm not giving Lewis a pass, he's been massively disappointing the last few years, but undoubtedly his inability to stay healthy has played a significant role. It's fair to question how much organizational instruction Lewis is actually absorbing at this point. I think it's entirely possible that the unsustainably hot start in a very SSS combined with the injuries set unreasonable expectations. That said, he hasn't been anything more than average-ish for short bursts the last 2 years and we're having serious discussions about whether he's worthy of arbitration, let alone an extension.
It very well could be that the Twins found a way to maximize the thing(s) some of the lesser prospects do well, and once big league pitching found a way to adjust, there was nothing there to counter with. Guys like the trio I mentioned weren't "can't miss," status. Brooks Lee might just be a subpar SS without a good hit tool. Again, I'm not giving this organization a pass, I think they've done a pretty poor job of developing players. What I'm saying is I don't know if there's actually some systemic issue that stops these young guys from blossoming at the MLB level, rather, the Twins might've squeezed all the metaphorical juice they could out of these guys, i.e. maybe it's a dearth of talent, and not a total failure in making the developmental jump from AAA to MLB.
Miranda and Julien will be interesting case studies this year.