Not meaningfully helpful: my parents have friends who have a condo in San Jose, and I think they've driven back and forth before. My mother went once and enjoyed it.
Now this is in my wheelhouse. As for lodging, to each his own, but I want to stay in the city center. Primarily because I want to go out and walk around, have dinner and some drinks and not have to drive anywhere to sleep. Heck, even without the drinks, I don't particularly like to drive at night either. But yes, you can get cheaper accomodations elsewhere.
My primary advice, generally not heeded by it's main recipients, is to slow down and drive less because you'll find there's lots to see and do in a smaller area. From your "at minimum" you're already way past that. That's a lot of territory to cover in 3 weeks and my advice would be to scale back.
You've also got a pretty long drive from Berlin to Nuremburg. Maybe your German friend has stops planned on the way, but I'd consider getting their via Prague, which is spectacular even if it's now overrun with Brits on stag and hen parties and not the quiet backwater it was the first time I was there in the '90s. If you were going that way, I'd hit
Cesky Krumlov, on the way to Vienna.
Of course, that would mean backtracking to get to Nuremburg, so maybe you don't want to go that way if Nuremburg is high on your list. Which would be entirely appropriate, especially if you're interested in the very good Nazi history museum, but even the old town is very cool too.
Not that it's really a recommendation, but the 12th century bridge in Regensburg is a family joke as our first trip with a camcorder featured disproportionate video of it.
If you're not going the Czech way, Rothenburg ob der Tauber is a tiny walled city that all the tour buses stop at. If you stay the night there, you can see it in a more leasurely way and it's pretty cool. It seems pretty corny but the
Night Watchman tour is actually fun (he's kinda funny).
ETA: I could write quite a bit about Munich, but I'll just put in a plug for the beer garden by the Chinese Tower in the Englisher Garden. The walk out there is nice and it's a good place for a beer and a umpah band. You can usually catch some urban
surfers here on the way too.
If you're driving from Munich to Vienna, Salzburg is a must stop. One of my favorite European things to do is hit the
Augustiner brewery in the monestary just down the river. The walk from the city center along the river to get there is nice too. And, of course, there's all of your Sound of Music sites and Mozart sites.
Moving on,
Hallstatt is beautiful and unspoilt. I love Vienna, although it's been awhile and I don't have any specific recommendations. (I do remember being really bored in the art museums as a kid, though I suspect I'd appreciate them more now). Take a tour of the Opera House.
Bratislava is pleasant and a bit quiet if you'e heading that way, but I wouldn't go at all out of the way to see it.
I've never been to Trieste, but if you're going in that direction,
Bled in Slovenia is pretty cool to my recollection (that was back in the '90s too, but the rest of my family was there two years ago and had good things to say).
Venice will be overrun with tourists and probably smelly. It's still totally worth it.
I've never been to Marseille proper, but I would recommend the French Riviera (duh). Cannes, St. Tropez and Nice are all good stops.
I'm assuming you're flying from Marseille to Dusseldorf? If not, you've got a lot more territory to cover and a lot more potential stops you could make.
ETA: On driving and parking, I personally wouldn't try to switch between driving and training. Unless you're going to stop in a particular city for several days, spending the time it takes to get to and from the rental agency isn't worth it. The beauty of European driving is that you can just follow the "city center" signs into town and then park in the first facility that strikes your fancy. Watch out for streetcars in Vienna though.
