Munich or Stuttgart Airport Easier to rent car to drive to Alps Southwest of Fussen?

I think you've answered your own question. Go for the smaller Stuttgart Airport.
The good thing about using Munich is that you can often fly all the way to North America from there--without having to go through another European gateway airport.
Ryanair doesn't fly into Stuttgart. Eurowings is the biggie there.

Check with viaMichelin about travel times by car. Many on here consider them the best guide for travel times with an auto. Also, I have read on here that it may take close to an hour to fill out the forms and pick up the car. It is a factor to figure.

If you are only going to Fussen, why not take the train from Munich? You could rent a car from Fussen and would save you the hassle of morning traffic. It is a two hour train trip from Munich. A Bayern ticket to Fussen would be 31 Euros, heading back to Munich would be more expensive.

Driving after an international flight has been compared to drunk driving on here.

It seems like MUC would make us drive across the city

Not exactly. From the airport you will bypass Munich in a big north-west semicircle along motorways no. 94 - 9 - 99 - 96 .

We would be driving back to the airport on a Monday morning.

From where will you drive back? I'd avoid that during rush hours (6-9pm), except when you arrive from the east (Regensburg, Landshut). Rather return the car the evening before departure and spend the night somewhere near the airport, e.g. in Freising or Erding (good public transport to the airport).

I tend to agree with csu. Have you explored rail connections to your destination? You didn't give your exact destination in the Alps SW of Füssen, but the Illertal is about where you describe. Once you get there you can purchase an Urlaubsticket which gives you access to all the trains and buses in the valley.

Both MUC and STR have convenient S-Bahn service into Munich Hbf or Stuttgart Hbf from which you can get trains to all over Bavaria. They take a little longer, but probably not much longer when you consider the time to rent a car. And getting there by train is so much more enjoyable and comfortable.

thanks for the advice so far! I'll check viaMichelin for drive times to see if that's more accurate than Google maps.

I can clarify a few things:

Location-wise in the Alps we are going somewhere we really loved, let's say around Reutte, Austria. I don't want to mention the name of the place because last time there we saw zero English speakers in 5 days. The name of the place has only been posted once on the Rick Steve's forum in half a million posts, and that was almost ten years ago! I won't be the person to change this place into the next overcrowded backdoor :)

We will be flying in from Paris or Nantes France, no jet lagged driving! Just trying to be more efficient than the train and we will be renting a car for Germany/the Alps anyway.

From what I'm hearing, maybe MUC isn't such a bad option compared to Stuttgart? The ring road around the city not so impacted, just avoid the morning rush hour on the day we return?

Is there a downside to Stuttgart though, 15km farther away but smaller airport and maybe more clear autobahn on the way?

Thanks again!

I've never driven to your little place from Munich (I think I may know where it is, actually...), so I can't comment on the drive from that direction. However, traffic around Stuttgart is never fun. Perhaps things have improved since I last drove it about three years ago, but from the Stuttgart airport, you would have to take A8 east. It can be touch-and-go around the city. The road then ascends into the Schwäbische Alb mountains, then splits as it traverses a series of bridges and a tunnel. The scenery is eye-popping, but unfortunately, traffic often snarls to a halt.

Tom hi - thanks for the helpful reply that traffic can be bad on either route. Definitely will take this into account.