If your toddler tolerates the car you could fly to MSP and drive to Rochester. I would rather drive than fly with my kids personally. It’s not even 1.5 hours from MSP to ROC and the drive is easy. Driving around Rochester is not bad at all. Mayo has valet parking you could use to help speed things up before and after appointments. There is an additional cost for valet, but I have never been charged for parking at my hotel so it may even out in the long run. Also, check VRBO for places close by that may family friendly than a hotel. Your stroller will be very helpful. Good luck on your trip and I wish you and your child safe travels!