Best Route Varenna to Bolzano

Best route by car: Varenna - Lecco - Bergamo - Verona - Bolzano
Best route by train: Varenna - Milano - Verona - Bolzano

A car alternative much loved on this website is the Stelvio route (Varenna - Sondrio - Bormio - Merano - Bolzano); very scenic, but very long and difficult to drive (84 hairpin curves on the pass section). The pass at present is still in its winter closure (generally open from late May to early October).

For scenery, I would rent a car and drive a mountain route. The main train and autostrada corridor from Milan to Verona and Venice is faster but boring. Bus would require several transfers and also focus on the more populated towns instead of the mountain route.

There are a couple of train routes, still a long way out of the way. The southern way would be to take a train to Lecco then a train to Bergamo, then a train to Brescia, then a train to Verona, then a train to Bolzano.
The northern route would be a train to Tirano then the Bernina Express or other trains to Chur, then a train to Buchs, then a train to Innsbruck, and finally a train to Bolzano.
The most direct route would be a train to Tirano, then a train to Pontresina, then a bus (#811) to Mal, then a train to Bolzano.
By car, the most direct route would be over the Passo d'Abrica to Edolo then on Rt 42 over Passo Tonale and the Mendel Pass into Bolzano.

We're traveling a similar route in October. The only difference - we're sleeping in Milan and day-tripping to Varenna. We plan to take the train from Milan to Bolzano (via Verona). We're renting a car in Bolzano and staying a few nights further north to enjoy the scenery. As we leave the Dolomites we'll be driving one of the scenic high mountain passes (Passo Falzarego) through Cortina d'Ampezzo and then south where we'll drop off our car at a town with a train station (probably Belluno) and then take the train to Venice.