Look for a direct flight from Venice to Dubrovnik (not every day) or maybe even Milan to Dubrovnik. Rent a car there as you leave town and drive to Plitvice (or take a long bus ride), drop the car in Zagreb, and fly home out of Zagreb if you can. If six days means five nights, then you might do two nights in Dubrovnik, one night in Plitvice, one night in Zagreb, and maybe one night elsewhere between Dubrovnik and Plitvice (e.g. Trogir, Split, Sibenik).
You're still going to lose a lot of time in transit between Siena and Dubrovnik. With only six days, some people might suggest you skip Croatia on this trip and spend the time in Italy instead instead of running around so much - or extend your time in Europe so you can spend more time in Croatia and be able to relax more.