You should definetely use the amazing OOTP Baseball for that purpose, more realistic sim engine over a longer term and way better stat tracking too.
On topic:
I'd say the Twins aren't the best example for a team needing a rebuild. I'm not following them much in real life but in The Show the are pretty much set for the future. Thier MLB roster is already pretty decent. All they need is a real ace and a quality BP arm or 2. Many of thier propects (Buxton, Sano Rosario, Meyer) all are close to being MLB ready. Mauer is a vquality player and has at least in the game 3 to 4 good years ahead of him so I'd keep him. Hunter could be traded if you take a more video game like approach, if you want to keep it close to real life let him retire as a Twin, it won't cost you much.